M. Karplus

发表

Molecular dynamics simulations in biology

M. Karplus, G. Petsko, 1990, Nature.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

M. Karplus, B. Brooks, R. Bruccoleri, 1983 .

Protein Folding: A Perspective from Theory and Experiment.

M. Karplus, C. Dobson, A. Sali, 1998, Angewandte Chemie.

Evaluation of comparative protein modeling by MODELLER

M. Karplus, A. Sali, Liz Potterton, 1995, Proteins.

Protein secondary structure prediction with a neural network.

M. Karplus, L. Holley, L. Howard, 1989, Proceedings of the National Academy of Sciences of the United States of America.

Method for estimating the configurational entropy of macromolecules

M. Karplus, J. Kushick, 1981 .

Genetic neural networks for quantitative structure-activity relationships: improvements and application of benzodiazepine affinity for benzodiazepine/GABAA receptors.

M. Karplus, S. So, Martin Karplus, 1996, Journal of medicinal chemistry.

Effective energy functions for protein structure prediction.

M. Karplus, T. Lazaridis, 2000, Current opinion in structural biology.

Kinetics of protein folding

M. Karplus, E. Shakhnovich, A. S˘ali, 1995, Nature.

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

M. Karplus, B. Brooks, 1983, Proceedings of the National Academy of Sciences of the United States of America.

Effective energy function for proteins in solution

M. Karplus, T. Lazaridis, 1999, Proteins.

Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state.

M. Karplus, D. Vitkup, Yaoqi Zhou, 1999, Journal of molecular biology.

Molecular dynamics simulations of biomolecules

J. Berg, M. Karplus, S. Gould, 2002, Nature Structural Biology.

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

Roland L. Dunbrack, M. Karplus, 1994, Nature Structural Biology.

Backbone-dependent rotamer library for proteins. Application to side-chain prediction.

Roland L. Dunbrack, M. Karplus, 1993, Journal of molecular biology.

An analysis of incorrectly folded protein models. Implications for structure predictions.

M. Karplus, R. Bruccoleri, J. Novotný, 1984, Journal of molecular biology.

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.

M. Karplus, B. Brooks, 1985, Proceedings of the National Academy of Sciences of the United States of America.

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Alexander D. MacKerell, M. Karplus, D. Nguyen, 1998, The journal of physical chemistry. B.

Increasing normal modes analysis accuracy: The SPASIBA spectroscopic force field introduced into the CHARMM program

M. Karplus, R. Stote, G. Vergoten, 2004 .

Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics

M. Karplus, C. Brooks, R. Austin, 1988 .

Diffusion–collision model for protein folding

M. Karplus, D. Weaver, 1979 .

Dynamics of folded proteins

M. Karplus, J. Mccammon, B. Gelin, 1977, Nature.

PDB-based protein loop prediction: parameters for selection and methods for optimization.

M. Karplus, H. V. van Vlijmen, H. Vlijmen, 1997, Journal of molecular biology.

Prediction of the folding of short polypeptide segments by uniform conformational sampling

M. Karplus, R. Bruccoleri, 1987, Biopolymers.

Interpreting the folding kinetics of helical proteins

M. Karplus, Yaoqi Zhou, 1999, Nature.

Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

M. Karplus, Yaoqi Zhou, Y. Zhou, 1999, Journal of molecular biology.

Crystallographic R Factor Refinement by Molecular Dynamics

M. Karplus, J. Kuriyan, Axel T. BR�NGER, 1987, Science.

CHARMM: The Energy Function and Its Parameterization

Alexander D. MacKerell, M. Karplus, B. Brooks, 2002 .

Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation

M. Karplus, D. Bashford, 1991 .

Molecular dynamics and protein function.

M. Karplus, J. Kuriyan, 2005, Proceedings of the National Academy of Sciences of the United States of America.

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.

M. Karplus, D. Bashford, 1990, Biochemistry.

Functionality maps of binding sites: A multiple copy simultaneous search method

M. Karplus, A. Miranker, 1991, Proteins.

Stochastic boundary conditions for molecular dynamics simulations of ST2 water

M. Karplus, C. Brooks, A. Brunger, 1984 .

Simulation of activation free energies in molecular systems

M. Karplus, S. Fischer, E. Neria, 1996 .

The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics

M. Karplus, O. Becker, 1997 .

Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom

M. Karplus, Stefan Fischer, 1992 .

Transition state contact orders correlate with protein folding rates.

M. Karplus, C. Dobson, K. Lindorff-Larsen, 2005, Journal of molecular biology.

X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin.

M. Karplus, A. Brünger, J. Kuriyan, 1989, Acta crystallographica. Section A, Foundations of crystallography.

SIMULATIONS OF MACROMOLECULES BY MULTIPLE TIME-STEP METHODS

M. Karplus, Masakatsu Watanabe, 1995 .

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

M. Karplus, B. Tidor, J. Gao, 1989, Science.

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

M. Karplus, T. Ichiye, 1991, Proteins.

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

M. Karplus, J. Evanseck, L. Caves, 1998, Protein science : a publication of the Protein Society.

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.

M. Karplus, B. Gelin, 1975, Proceedings of the National Academy of Sciences of the United States of America.

Discrimination of the native from misfolded protein models with an energy function including implicit solvation.

M. Karplus, T. Lazaridis, 1999, Journal of molecular biology.

Crystallographic refinement by simulated annealing: application to crambin

M. Karplus, G. Petsko, A. Brunger, 1989 .

A Comprehensive Analytical Treatment of Continuum Electrostatics

M. Karplus, Michael Schaefer and, 1996 .

Guide to Biomolecular Simulations

M. Karplus, O. Becker, 2005 .

Advances in chemical physics, volume 71: Proteins: A theoretical perspective of dynamics, structure, and thermodynamics

M. Karplus, C. Brooks, B. Pettitt, 2006 .

Deformable stochastic boundaries in molecular dynamics

M. Karplus, C. Brooks, 1983 .

Combining ab initio and density functional theories with semiempirical methods

M. Karplus, Q. Cui, Hong Guo, 2002 .

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

M. Karplus, M. Field, P. Bash, 1990 .

Allostery and cooperativity revisited

M. Karplus, Q. Cui, 2008, Protein science : a publication of the Protein Society.

A gating mechanism of pentameric ligand-gated ion channels

Antoine Taly, Marco Cecchini, Martin Karplus, 2013, Proceedings of the National Academy of Sciences.

Conformational Free-Energy Difference of a Miniprotein from Nonequilibrium Simulations

M. Karplus, M. Cecchini, M. Spichty, 2010 .

Segmented transition pathway of the signaling protein nitrogen regulatory protein C.

Martin Karplus, M. Karplus, D. Kern, 2009, Journal of molecular biology.

A mathematical model for structure-function relations in hemoglobin.

M Karplus, M. Karplus, A. Szabó, 1972, Journal of molecular biology.

Structure-specific model of hemoglobin cooperativity.

M. Karplus, A. W. Lee, A. W. Lee, 1983, Proceedings of the National Academy of Sciences of the United States of America.

Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative mechanism.

M Karplus, M. Karplus, B. Gelin, 1983, Journal of molecular biology.

A Dynamic Model for the Allosteric Mechanism of GroEL

M Karplus, P B Sigler, M. Karplus, 2000 .

Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior

Martin Karplus, M. Karplus, 2000 .

The unfolding action of GroEL on a protein substrate.

Jianpeng Ma, Martin Karplus, M. Karplus, 2004, Biophysical journal.

Biomolecular motors: the F1-ATPase paradigm.

Martin Karplus, Yi Qin Gao, M. Karplus, 2004, Current opinion in structural biology.

A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase.

Jianpeng Ma, Martin Karplus, Qiang Cui, 2004, Journal of molecular biology.

"New view" of protein folding reconciled with the old through multiple unfolding simulations.

M Karplus, M. Karplus, T. Lazaridis, 1997, Science.

Significance of Molecular Dynamics Simulations for Life Sciences

Richard Lavery, Martin Karplus, M. Karplus, 2014 .

Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids

B. Montgomery Pettitt, Charles L. Brooks, Martin Karplus, 1985 .

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA

Wei Yang, Gregory L. Verdine, Martin Karplus, 2005, Nature.

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.

M. Karplus, R. Elber, 1987, Science.

An all-atom empirical energy function for the simulation of nucleic acids

Alexander D. MacKerell, M. Karplus, J. Wiórkiewicz-Kuczera, 1995 .

Molecular anatomy of the antibody binding site.

M Karplus, M. Karplus, R. Bruccoleri, 1983, The Journal of biological chemistry.

Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin

M Karplus, M. Karplus, T. Lazaridis, 1997, Protein science : a publication of the Protein Society.

Simulation analysis of the stability mutant R96H of T4 lysozyme.

M Karplus, B Tidor, M. Karplus, 1991, Biochemistry.

Enhanced chemical synthesis at soft interfaces: a universal reaction-adsorption mechanism in microcompartments.

Andrew D Griffiths, Martin Karplus, Thomas Mangeat, 2014, Physical review letters.

The Proton Sponge: a Trick to Enter Cells the Viruses Did Not Exploit

Roland L. Dunbrack, M. Karplus, C. Schiffer, 1997, CHIMIA.

Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin

Collin M. Stultz, M Karplus, M. Karplus, 2000, Proteins.

Improving the accuracy of protein pKa calculations: Conformational averaging versus the average structure

M Karplus, M. Karplus, H. V. van Vlijmen, 1998, Proteins.

Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics.

M Karplus, M. Karplus, T. Lazaridis, 1995, Advances in protein chemistry.

Empirical energy functions for energy minimization and dynamics of nucleic acids

Lennart Nilsson, Martin Karplus, M. Karplus, 1986 .

Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison

M Karplus, A T Brünger, M. Karplus, 1988, Proteins.

Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox

Joe Marks, J. Thomas Ngo, Martin Karplus, 1994 .

Native and non‐native interactions along protein folding and unfolding pathways

Michele Vendruscolo, Emanuele Paci, Martin Karplus, 2002, Proteins.

Dynamics of proteins: elements and function.

M Karplus, J A McCammon, M. Karplus, 1983, Annual review of biochemistry.

Domain association in immunoglobulin molecules. The packing of variable domains.

C. Chothia, M. Karplus, R. Bruccoleri, 1985, Journal of molecular biology.

A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method

Efthimios Kaxiras, Martin Karplus, Marcus Elstner, 2001 .

The human cytomegalovirus UL44 C clamp wraps around DNA.

M. Karplus, D. Filman, R. Petrella, 2008, Structure.

Protein-folding dynamics

M. Karplus, D. Weaver, 1976, Nature.

A method for constrained energy minimization of macromolecules

M. Karplus, W. V. van Gunsteren, W. V. Gunsteren, 1980 .

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study.

M. Karplus, W. V. van Gunsteren, Martin Karplus, 1982, Biochemistry.

Parametrization of the friction constant for stochastic simulations of polymers

M. Karplus, R. Pastor, 1988 .

A mechanism for rotamase catalysis by the FK506 binding protein (FKBP).

M. Karplus, S. Fischer, S. Michnick, 1993, Biochemistry.

Cis-Trans Imide Isomerization of the Proline Dipeptide

Roland L. Dunbrack, M. Karplus, Stefan Fischer, 1994 .

Contact Electron‐Spin Coupling of Nuclear Magnetic Moments

M. Karplus, 1959 .

Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution

M. Karplus, M. Blackledge, R. R. Ernst, 1992 .

Three key residues form a critical contact network in a protein folding transition state

M. Karplus, C. Dobson, E. Paci, 2001, Nature.

Determination of a transition state at atomic resolution from protein engineering data.

M. Karplus, C. Dobson, E. Paci, 2002, Journal of molecular biology.

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all‐atom molecular dynamics simulations with ϕ value restraints

M. Karplus, S. Radford, K. Lindorff-Larsen, 2003, Proteins.

An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications

Alexander D. MacKerell, M. Karplus, J. Brickmann, 1996 .

Understanding beta-hairpin formation.

M. Karplus, T. Lazaridis, A. Dinner, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide.

S. F. Chekmarev, M. Karplus, S. Krivov, 2002, Physical review letters.

Simulation of protein misfolding using a lattice model

S. F. Chekmarev, M. Karplus, I. Titov, 2006 .

Understanding protein folding via free-energy surfaces from theory and experiment.

Lorna J. Smith, M. Karplus, C. Dobson, 2000, Trends in biochemical sciences.

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

M. Karplus, C. Bartels, M. Schaefer, 1998, Journal of molecular biology.

Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane

M. Karplus, B. Roux, 1993 .

Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements.

J. D. Morgan, M. Karplus, J. Mccammon, 1981, Journal of molecular biology.

Does lysozyme follow the lysozyme pathway? An alternative based on dynamic, structural, and stereoelectronic considerations

M. Karplus, C. Post, 1986 .

Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics simulation

M. Karplus, T. Ichiye, 1987, Proteins.

The signaling pathway of rhodopsin.

M. Karplus, Y. Kong, Yifei Kong, 2007, Structure.

Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis

M. Karplus, Y. Kong, Yifei Kong, 2009, Proteins.

Quantum-mechanical study of H + H2 reactive scattering

M. Karplus, K. Tang, 1967 .

Development of multiscale models for complex chemical systems: from H+H₂ to biomolecules (Nobel Lecture).

M. Karplus, 2014, Angewandte Chemie.

Folding of a SH3 domain: standard and "hydrodynamic" analyses.

S. F. Chekmarev, M. Karplus, I. Kalgin, 2009, The journal of physical chemistry. B.

Behind the folding funnel diagram.

M. Karplus, 2011, Nature chemical biology.

Atoms and Molecules: An Introduction for Students of Physical Chemistry

M. Karplus, R. Porter, 1970 .

The hinge-bending mode in lysozyme

M. Karplus, P. Wolynes, J. Mccammon, 1976, Nature.

Dynamics of ligand binding to heme proteins.

M. Karplus, D. Case, M. Karplus, 1979, Journal of molecular biology.

Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin

M. Karplus, R. Elber, 1990 .

Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix

M. Karplus, J. Kushick, R. Levy, 1984 .

The hinge‐bending mode of a lysozyme–inhibitor complex

M. Karplus, R. Bruccoleri, J. Mccammon, 1986, Biopolymers.

Folding thermodynamics of a model three-helix-bundle protein.

M. Karplus, Yaoqi Zhou, Y. Zhou, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Triosephosphate isomerase: a theoretical comparison of alternative pathways.

M. Karplus, Q. Cui, 2001, Journal of the American Chemical Society.

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants.

M. Karplus, Q. Cui, 2002, Journal of the American Chemical Society.

Quantum Mechanical / Molecular Mechanical Studies of the Triosephosphate Isomerase-Catalyzed Reaction : Verification of Methodology and Analysis of Reaction Mechanisms

M. Karplus, Qiang Cui† and, Qiang Cui, 2022 .

Protein Folding: A Perspective from Theory and Experiment

M. Karplus, C. Dobson, A. Sali, 1998 .

THE THERMODYNAMICS AND KINETICS OF PROTEIN FOLDING : A LATTICE MODEL ANALYSIS OF MULTIPLE PATHWAYS WITH INTERMEDIATES

M. Karplus, A. Dinner, 1999 .

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

M. Karplus, E. Shakhnovich, A. Sali, 1994, Journal of molecular biology.

Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions

M. Karplus, Yaoqi Zhou, C. Hall, 1997 .

How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations

M. Karplus, D. Truhlar, Jiali Gao, 2004, Science.

Internal motions of antibody molecules

M. Karplus, J. Mccammon, 1977, Nature.

Hidden complexity of free energy surfaces for peptide (protein) folding.

M. Karplus, S. Krivov, 2004, Proceedings of the National Academy of Sciences of the United States of America.

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

M. Karplus, D. Kern, M. Lei, 2007, Nature.

A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)

Martin Karplus, Marcus Elstner, Qiang Cui, 2002 .

On the calculation of entropy from covariance matrices of the atomic fluctuations

Ioan Andricioaei, Martin Karplus, M. Karplus, 2001 .

Molecular dynamics of biological macromolecules: A brief history and perspective

Martin Karplus, M. Karplus, 2003, Biopolymers.

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.

Martin Karplus, Paul Maragakis, M. Karplus, 2005, Journal of molecular biology.

Intrinsic motions along an enzymatic reaction trajectory

Mark A. Wilson, Martin Karplus, Gregory A. Petsko, 2007, Nature.

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations.

M Karplus, E Paci, M. Karplus, 1999, Journal of molecular biology.

Empirical force field study of geometries and conformational transitions of some organic molecules

Martin Karplus, Jeremy C. Smith, M. Karplus, 1992 .

The energetics of off-rotamer protein side-chain conformations.

M Karplus, M. Karplus, R. Petrella, 2001, Journal of molecular biology.

Structures of scrambled disulfide forms of the potato carboxypeptidase inhibitor predicted by molecular dynamics simulations with constraints

M. Karplus, M. Martí-Renom, R. Stote, 2000, Proteins.

Orientational correlations and entropy in liquid water

Themis Lazaridis, Martin Karplus, M. Karplus, 1996 .

Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

M. Karplus, M. Meuwly, P. Gupta, 2019, eLife.

Modeling of the TCR-MHC-peptide complex.

M Karplus, M. Karplus, O. Michielin, 2000, Journal of molecular biology.

Abinitio force field for the planar vibrations of benzene

M. Karplus, Hong Guo, 1988 .

Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

M Karplus, G A Petsko, M. Karplus, 1990, Science.

Absolute pKa calculations with continuum dielectric methods

Carmay Lim, Martin Karplus, M. Karplus, 1991 .

pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis.

Alexander D. MacKerell, M Karplus, M. Karplus, 1995, Journal of molecular biology.

pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences between Conformations†

Martin Karplus, M. Karplus, M. Schaefer, 1997 .

Free energy simulations come of age: protein-ligand recognition.

Thomas Simonson, Martin Karplus, Georgios Archontis, 2002, Accounts of chemical research.

Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural networks.

M Karplus, M. Karplus, S. So, 1996, Journal of medicinal chemistry.

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

M Karplus, M. Karplus, V. Zoete, 2002, Journal of molecular biology.

Analysis of side-chain orientations in homologous proteins.

M Karplus, M. Karplus, N. Summers, 1987, Journal of molecular biology.

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.

M Karplus, M. Karplus, T. Simonson, 2001, Journal of molecular biology.

Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins

Martin Karplus, Wonmuk Hwang, M. Karplus, 2019, Proceedings of the National Academy of Sciences.

Zinc binding in proteins and solution: A simple but accurate nonbonded representation

M Karplus, M. Karplus, R. Stote, 1995, Proteins.

Theoretical studies of protein folding and unfolding.

M Karplus, A Sali, M. Karplus, 1995, Current opinion in structural biology.

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase.

M. Karplus, A. Caflisch, A. Miranker, 1993, Journal of medicinal chemistry.

Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs

M Karplus, M. Karplus, D. Joseph-McCarthy, 1997, Proteins.

An automated method for dynamic ligand design

M Karplus, M. Karplus, A. Miranker, 1995, Proteins.

Computational combinatorial chemistry for de novo ligand design: Review and assessment

Amedeo Caflisch, Martin Karplus, M. Karplus, 1995 .

SOLVATION. A MOLECULAR DYNAMICS STUDY OF A DIPEPTIDE IN WATER.

Martin Karplus, Peter J. Rossky, M. Karplus, 1979 .

Molecular dynamics of ferrocytochrome c

M. Karplus, J. Mccammon, M. Pear, 1980, Nature.

Integral equation model for aqueous solvatlon of polyatomic solutes: Application to the determination of the free energy surface for the internal motion of biomolecules

M. Karplus, P. Rossky, B. Pettitt, 1986 .

HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

M Karplus, R E Hubbard, M B Eisen, 1994, Proteins.

Dynamic Aspects of Protein Structure

Martin Karplus, M. Karplus, 1985 .

The HSP90 binding mode of a radicicol-like E-oxime determined by docking, binding free energy estimations, and NMR 15N chemical shifts.

M. Karplus, H. Kessler, A. Taly, 2009, Biophysical chemistry.

Role of Conformational Heterogeneity in Domain Swapping and Adapter Function of the Cks Proteins*

M. Karplus, M. Bycroft, L. Itzhaki, 2005, Journal of Biological Chemistry.

Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.

M Karplus, M. Karplus, J. Ma, 1997, Journal of molecular biology.

Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential

Martin J. Field, Martin Karplus, Paul A. Bash, 1987 .

Exploration of disorder in protein structures by X‐ray restrained molecular dynamics

John Kuriyan, Martin Karplus, M. Karplus, 1991, Proteins.

Ligand binding and protein relaxation in heme proteins: a room temperature analysis of nitric oxide geminate recombination

Krzysztof Kuczera, Jacob W. Petrich, Martin Karplus, 1991 .

Temperature dependence of the structure and dynamics of myoglobin. A simulation approach.

M Karplus, J Kuriyan, M. Karplus, 1990, Journal of molecular biology.

Estimation of uncertainties in X‐ray refinement results by use of perturbed structures

M Karplus, J Kuriyan, G A Petsko, 1987, Proteins.

Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics.

M Karplus, J Kuriyan, G A Petsko, 1986, Journal of molecular biology.

Binding of oxygen and carbon monoxide to hemoglobin. An analysis of the ground and excited states

D. A. Case, M. Karplus, D. Case, 1979 .

Demonstration by NMR of folding domains in lysozyme

Christopher M. Dobson, Sheena E. Radford, Martin Karplus, 1991, Nature.

Application of the diffusion-collision model to the folding of three-helix bundle proteins.

Martin Karplus, David L Weaver, Suhail A Islam, 2002, Journal of molecular biology.

Molecular dynamics simulations with experimental restraints

Martin Karplus, M. Karplus, Axel T. Bruenger, 1991 .

Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin.

M Karplus, M. Karplus, N. Summers, 1989, Journal of molecular biology.

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.

M Karplus, C L Brooks, M. Karplus, 1989, Journal of molecular biology.

Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study.

M Karplus, K Schulten, J Deisenhofer, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Electric Polarizability of Some Diatomic Molecules

M. Karplus, H. Kolker, 1963 .

Time‐Dependent Variation‐Perturbation Method for Many‐Electron Systems

M. Karplus, H. Kolker, 1963 .

Magnetic Properties of Hydrogen Fluoride. II. Susceptibility

T. P. Das, M. Karplus, R. P. Hurst, 1962 .

Title: Modeling Atomic Structure of the Emre Multidrug Pump to Design Inhibitor Peptides

M. Karplus, V. Ovchinnikov, 2022 .

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

Martin Karplus, M. Karplus, A. van der Vaart, 2007, The Journal of chemical physics.

Exchange Reactions with Activation Energy. I. Simple Barrier Potential for (H, H2)

Martin Karplus, R. N. Porter, M. Karplus, 1965 .

Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan binding regions and protease-specific antigenic epitopes.

M Karplus, A Sali, H P McNeil, 1993, The Journal of biological chemistry.

Diffusive langevin dynamics of model alkanes

J. Andrew McCammon, Ronald M. Levy, Martin Karplus, 1979 .

Molecular Mechanics and Dynamics Simulations of Enzymes

M. Karplus, R. Stote, A. Dejaegere, 2002 .

The Jacobian factor in free energy simulations

M. Karplus, S. Boresch, 1996 .

Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway.

M Karplus, G A Petsko, M. Karplus, 1991, Biochemistry.

Simulations of enzymic reactions.

M. Karplus, A. Mulholland, 1996, Biochemical Society transactions.

A simplified confinement method for calculating absolute free energies and free energy and entropy differences.

M. Karplus, M. Cecchini, V. Ovchinnikov, 2013, The journal of physical chemistry. B.

Implications of alternative substrate binding modes for catalysis by uracil-DNA glycosylase: an apparent discrepancy resolved.

M. Karplus, Ao Ma, A. Dinner, 2006, Biochemistry.

Internal and Overall Peptide Group Motion in Proteins: Molecular Dynamics Simulations for Lysozyme Compared with Results from X-ray and NMR Spectroscopy

Matthias Buck, Martin Karplus, M. Karplus, 1999 .

Chapter 2 Application of Padé Approximants to Dispersion Force and Optical Polarizability Computations

P. W. Langhoff, M. Karplus, 1970 .

Retarded van der Waals Interactions. I. Simple Atoms

M. Karplus, P. M. Getzin, 1970 .

Normal mode analysis of large systems with icosahedral symmetry: Application to (Dialanine)60 in full and reduced basis set implementations

M. Karplus, H. V. Vlijmen, H. Vlijmen, 2001 .

Theoretical study of the ground‐state vibrations of the linear polyenes

M. Karplus, B. Brooks, R. Hemley, 1986 .

THE ANALYSIS OF MOLECULAR WAVE FUNCTIONS BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY1a

M. Karplus, 1960 .

A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin

M. Karplus, G. Petsko, D. Vitkup, 1997, Nature Structural Biology.

Heme—Iron Ligand Binding

M. Karplus, 1982 .

The calculation of two-electron properties from multiple-scattering Xα wavefunctions

M. Karplus, M. Cook, 1981 .

Study of the insulin dimerization: Binding free energy calculations and per‐residue free energy decomposition

Markus Meuwly, Vincent Zoete, Martin Karplus, 2005, Proteins.

Kinesin motility is driven by subdomain dynamics

M. Karplus, W. Hwang, M. Lang, 2017, eLife.

Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging

M. Karplus, J. Mccammon, R. Levy, 1981 .

Structure activity relationship by NMR and by computer: a comparative study.

Nicolas Froloff, Finton Sirockin, Martin Karplus, 2002, Journal of the American Chemical Society.

The interpretation of site-directed mutagenesis experiments by linear free energy relations.

M. Karplus, J. Straub, 1990, Protein engineering.

Magnetic Properties and Dipole Moment of CO

M. Karplus, R. Stevens, R. M. Stevens, 1968 .

Mechanical coupling in myosin V: a simulation study.

M. Karplus, B. Trout, V. Ovchinnikov, 2009, Journal of molecular biology.

Angular Dependence of Electron‐Coupled Proton Interactions in CH2 Groups

H. S. Gutowsky, M. Karplus, D. Grant, 1959 .

The normal modes of the gramicidin-A dimer channel.

M Karplus, M. Karplus, B. Roux, 1988, Biophysical journal.

Active site dynamics of ribonuclease.

M Karplus, C L Brooks, A T Brünger, 1985, Proceedings of the National Academy of Sciences of the United States of America.

Spinach on the ceiling: a theoretical chemist's return to biology.

M. Karplus, 2006, Annual review of biophysics and biomolecular structure.

Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra.

M Karplus, M. Karplus, K. Kuczera, 1990, Proceedings of the National Academy of Sciences of the United States of America.

Ion transport in a gramicidin-like channel: dynamics and mobility

Benoît Roux, Martin Karplus, M. Karplus, 1991 .

Approximations to Hartree—Fock Perturbation Theory

P. W. Langhoff, M. Karplus, R. P. Hurst, 1966 .

Dianionic pentacoordinate species in the base-catalyzed hydrolysis of ethylene and dimethyl phosphate

M. Karplus, C. Lim, A. Dejaegere, 1991 .

The Anomeric Equilibrium in d-Xylose: Free Energy and the Role of Solvent Structuring

M. Karplus, J. Brady, R. Schmidt, 1996 .

Refractive Index of the Hydrogen Molecule

M. Karplus, 1964 .

Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations

Martin J. Field, Martin Karplus, Gerald R. Kneller, 1991 .

Effective coupling in bridged electron transfer molecules: Computational formulation and examples

M. Karplus, J. Evenson, 1992 .

Multiple Conformational States of Myoglobin: A Molecular Dynamics Analysis

M. Karplus, R. Elber, R. Elber, 1987 .

Proton Spin Coupling by Pi Electrons

M. Karplus, 1960 .

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations.

M Karplus, M. Karplus, D. Moras, 1998, Journal of molecular biology.

Retinoic acid receptor: a simulation analysis of retinoic acid binding and the resulting conformational changes.

M Karplus, M. Karplus, S. Fischer, 1999, Journal of molecular biology.

Asymmetric synthesis of pochonin E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors.

M. Karplus, V. Zoete, C. Zambaldo, 2012, Chemistry.

Packaging of Proteases and Proteoglycans in the Granules of Mast Cells and Other Hematopoietic Cells

Richard L. Stevens, Martin Karplus, M. Karplus, 1995, The Journal of Biological Chemistry.

Structures and relative free energies of partially folded states of proteins

M. Karplus, C. Dobson, E. Paci, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation.

M. Karplus, C. Dobson, L. J. Smith, 2001, Journal of molecular biology.

A CRITERION FOR ORBITAL HYBRIDIZATION AND CHARGE DISTRIBUTION IN CHEMICAL BONDS.

M. Karplus, D. Grant, 1959, Proceedings of the National Academy of Sciences of the United States of America.

Coexisting origins of subdiffusion in internal dynamics of proteins.

M. Karplus, Yasmine Meroz, V. Ovchinnikov, 2017, Physical review. E.

The HSP90 binding mode of a radicicol-like -oxime from docking, binding free energy estimations, and NMR N chemical shifts

M. Karplus, H. Kessler, A. Taly, 2020 .

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

M. Karplus, A. Chakraborty, J. Barton, 2018, eLife.

Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site

M. Karplus, A. Chakraborty, D. Burton, 2021, Proceedings of the National Academy of Sciences.

A kinetic model of coordinated myosin V.

M. Karplus, Y. Gao, Yudong Wu, 2007, Biochemistry.

Restraints in temperature-factor refinement for macromolecules: an evaluation by molecuar dynamics

M. Karplus, W. Hendrickson, Hai-Bo Yu, 1985 .

MOLECULAR DYNAMICS SIMULATION OF THE PRIMARY PROCESSES IN THE PHOTOSYNTHETIC REACTION CENTER OF Rhcdopseudomonas viridis

M. Karplus, J. Deisenhofer, K. Schulten, 2022 .

Dynamics of Ligand Binding to Proteins

M. Karplus, 1986 .

Solvent mobility and the protein 'glass' transition

Dagmar Ringe, Dennis Vitkup, Martin Karplus, 2000, Nature Structural Biology.

The structural enzymology of proton-transfer reactions

John Alan Gerlt, Dagmar Ringe, Martin Karplus, 1993 .

Why protein R‐factors are so large: A self‐consistent analysis

Gregory A Petsko, Dagmar Ringe, Dennis Vitkup, 2002, Proteins.

Alkaline Hydrolysis of Amide Bonds: Effect of Bond Twist and Nitrogen Pyramidalization

M. Karplus, X. López, G. Blackburn, 2003 .

Synthesis of a novel diarylphosphinic acid: a distorted ground state mimic and transition state analogue for amide hydrolysis

M. Karplus, X. López, V. Gouverneur, 2001 .

Determination of the pKaof the 2‘-Hydroxyl Group of a Phosphorylated Ribose: Implications for the Mechanism of Hammerhead Ribozyme Catalysis

M. Karplus, P. Lyne, 2000 .

A metastable state in folding simulations of a protein model

M. Karplus, A. Dinner, 1998, Nature Structural Biology.

Theoretical Investigations of Reactive Collisions in Molecular Beams: K+CH3I and Related Systems

M. Karplus, L. Raff, 1966 .

Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin

M Karplus, M. Karplus, S. Schreiber, 1991, Science.

Molecular Dynamics Simulation of the Primary Processes in the Photosynthetic Reaction Center of Rhodopseudomonas Viridis

Klaus Schulten, C. Niedermeier, Herbert R. Treutlein, 1988 .

Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

Eric Vanden-Eijnden, Victor Ovchinnikov, Martin Karplus, 2011, The Journal of chemical physics.

Optimal estimates of free energies from multistate nonequilibrium work data.

M. Karplus, P. Maragakis, M. Spichty, 2006, Physical review letters.

Nature of the iron-oxygen bond in oxyhemoglobin.

M. Karplus, D. Case, B. H. Huynh, 1977, Journal of the American Chemical Society.

PROTEIN-PROTEIN INTERACTIONS IN DNA RECOGNITION 'H-Nuclear Magnetic Resonance Studies of X cI Repressors Genetically Altered by Site-Directed Mutagenesis

M. Karplus, M. Weiss, R. Stearman, 2005 .

Conformation of retinal isomers.

M. Karplus, B. Sykes, R. Rowan, 1974, Biochemistry.

The enumeration of Goldstone diagrams in many-body perturbation theory

M. Karplus, P. Rossky, 1976 .

Comparison of Accurate Quantum‐Mechanical Probabilities with Classical and Transition‐State Theory Results for the Collinear Exchange Reaction H + H2 → H2 + H

M. Karplus, D. J. Diestler, 1971 .

Electronic structure of the MoFe3S4(SH)3−6 ion: A broken‐symmetry metal–sulfur cluster

M. Karplus, M. Cook, 1985 .

QUANTUM THEORY OF (H,H$sub 2$) SCATTERING: APPROXIMATE TREATMENTS OF REACTIVE SCATTERING.

M. Karplus, K. Tang, 1971 .

Quantum Mechanics of Simple Chemical Reactions

M. Karplus, 1974 .

THEORETICAL INTERPRETATION OF CARBON-13 HYPERFINE INTERACTIONS IN ELECTRON SPIN RESONANCE SPECTRA. Technical Note Report No. 9

M. Karplus, G. Fraenkel, 1961 .

Eleventh breeding-bird census. 13. Damp deciduous scrub with numerous standing dead trees

C. S. Robbins, M. Karplus, R. Stewart, 1947 .

Potential Energy Surface for H3

M. Karplus, R. Porter, 1964 .

Energy Dependence of Cross Sections for Hot Tritium Reactions with Hydrogen and Deuterium Molecules

M. Karplus, R. Porter, R. Sharma, 1966 .

Quadrupole Moment of Ethane

M. Karplus, O. Sovers, C. W. Kern, 1966 .

The self-consistent random phase approximation

M. Karplus, N. Ostlund, 1971 .

Differential Cross Sections for D+H2: A Comparison with Experiment

M. Karplus, P. Brumer, 1971 .

Collision complex dynamics in alkali halide exchange reactions

M. Karplus, P. Brumer, 1973 .

Bond-function analysis of rotational barriers: Methanol

M. Karplus, O. Sovers, C. W. Kern, 1968 .

Erratum: Kinetics of diffusion‐influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions [J. Chem. Phys. 86, 1883 (1987)]

M. Karplus, Sangyoub Lee, 1992 .

1H-NMR study of the λ operator site OL1: assignment of the imino and adenine H2 resonances

M. Karplus, R. Sauer, D. Patel, 1984 .

β‐Proton Hyperfine Splittings in the Vinyl Radical

M. Karplus, F. Adrian, 1964 .

Orbital Following in the Methyl Radical

M. Karplus, D. M. Schrader, 1964 .

Spin Resonance Spectra of Substituted Aromatic Ions: Perturbation Model

M. Karplus, J. Schug, T. H. Brown, 1962 .

Theory of the Spin and Charge Distribution in Aromatic Ion Radicals; Application to the Naphthalene Negative Ion

M. Karplus, J. Schug, T. H. Brown, 1961 .

Interpretation of the Electron‐Spin Resonance Spectrum of the Methyl Radical

M. Karplus, 1959 .

A model for electrostatic effects in proteins

David J. States, Martin Karplus, M. Karplus, 1987 .

Xα multiple scattering calculations on iron(II) porphine

M. Karplus, D. Case, S. Sontum, 1983 .

X‐ray structural and simulation analysis of a protein mutant: The value of a combined approach

M. Karplus, B. Tidor, C. Mattos, 2004, Proteins.

Convergence of valence bond and molecular orbital theories

M. Karplus, W. Campion, 1973 .

ppdx: Automated modeling of protein–protein interaction descriptors for use with machine learning

M. Karplus, Simone Conti, V. Ovchinnikov, 2022, J. Comput. Chem..

Multistructure Valence‐Bond and Atoms‐in‐Molecules Calculations for LiF, F2, and F2−

M. Karplus, G. G. Balint-Kurti, 1969 .

Calculation of one-electron properties for the formaldehyde molecule with the LCAO MO SCF function of Foster and Boys.

M. Karplus, G. Kerley, S. Chan, 1966, The Journal of chemical physics.

Deuteron Quadrupole Coupling in Diatomic ``Hydrides''

M. Karplus, H. Kolker, 1962 .

Structure of CH3 and CF3

M. Karplus, K. Morokuma, L. Pedersen, 1968 .

Padé Summation of the Cauchy Dispersion Equation

P. W. Langhoff, M. Karplus, 1969 .

Correlation energy contribution to the ammonia inversion barrier

N. C. Dutta, M. Karplus, 1975 .

A theoretical investigation of the AlC2H4 complex

M. Karplus, Jiali Gao, 1990 .

Comparison of 3D Classical Trajectory and Transition‐State Theory Reaction Cross Sections

M. Karplus, G. Koeppl, 1971 .

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

Olivier Michielin, Vincent Zoete, Martin Karplus, 2003, J. Comput. Aided Mol. Des..

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Martin Karplus, Carlos Bustamante, Paul Maragakis, 2007, The Journal of chemical physics.

Methyl group inductive effect in the toluene ions. Comparison of Hueckel and extended Hueckel theory

M. Karplus, D. Purins, 1968 .

Electron correlation and density-functional methods

M. Karplus, M. Cook, 1987 .

PROTEIN FOLDING AND MISFOLDING: A BIFURCATION STUDY OF A LATTICE MODEL

M. Karplus, Sb Ras, S. Chekmarev, 2004 .

Comment: Reinterpretation of hexatriene spectrum and comparison with theory

M. Karplus, S. Rice, R. M. Gavin, 1975 .

Variation‐Perturbation Approach to the Interaction of Radiation with Matter

M. Karplus, 1962 .

Exploratory search during directed navigation in C. elegans and Drosophila larva

Aravinthan D. T. Samuel, Anggie J. Ferrer, M. Karplus, 2017, eLife.

Exploratory search during directed navigation in C

Aravinthan D. T. Samuel, Anggie J. Ferrer, M. Karplus, 2017 .

Nuclear Magnetic Resonance Determination of the Angle Ψ in Peptides

M. Karplus, S. Karplus, 1972 .

Valence-bond bond-order formulation for contact nuclear spin-spin coupling

M. Karplus, M. Barfield, 1969 .

Mechanism of tertiary structural change in hemoglobin (cooperativity/protein dynamics/stereochemical trigger/conformational energy calculations)

M. Karplus, B. Gelin, 2016 .

Molecular dynamics simulations of biomolecules.

Martin Karplus, M. Karplus, J. Mccammon, 2002, Nature structural biology.

Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain.

M. Karplus, A. Brünger, R. Huber, 1987, Biochemistry.

The dynamics of proteins.

M Karplus, J A McCammon, M. Karplus, 1986, Scientific American.

Vicinal Proton Coupling in Nuclear Magnetic Resonance

Martin Karplus, M. Karplus, 1963 .

Bird Activity in the Continuous Daylight of Arctic Summer

M. Karplus, 1952 .

Xalpha multiple scattering calculations on copper porphine.

M. Karplus, D. Case, 1977, Journal of the American Chemical Society.

Aqueous solvation of N-methylacetamide conformers: comparison of simulations and integral equation theories

M. Karplus, B. Pettitt, Hsiang‐Ai Yu, 1991 .

Uracil-DNA glycosylase acts by substrate autocatalysis

Aaron R. Dinner, Martin Karplus, G. Michael Blackburn, 2001, Nature.

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems.

M. Karplus, D. York, X. López, 2006, The journal of physical chemistry. B.

Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis.

M. Karplus, X. López, M. Schaefer, 2002, Journal of the American Chemical Society.

Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.

M. Karplus, K. Kuczera, J. Martin, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved

Adrian J. Mulholland, Martin Karplus, M. Karplus, 2000 .

Ligand Influence upon Radial Wave Functions

M. Karplus, R. Belford, 1959 .

Application of Xα multiple-scattering theory to planar organic molecules: One-electron properties and ionization potentials of benzene, pyridine, pyrazine, pyrrole, and imidazole

M. Karplus, D. Case, M. Cook, 1980 .

Xα MULTIPLE SCATTERING CALCULATIONS ON COPPER PORPHINE

M. Karplus, D. Case, 1977 .

Valence‐Bond Interpretation of Electron‐Coupled Nuclear Spin Interactions; Application to Methane

M. Karplus, D. H. Anderson, 1959 .

Hydrolysis rate difference between cyclic and acyclic phosphate esters: solvation versus strain

M. Karplus, A. Dejaegere, 1993 .

Ab initio studies of methylated 1,3-butadienes

M. Karplus, Hong Guo, 1992 .

Studies of Zero‐Field Splittings in Aromatic Molecules

M. Karplus, C. W. Kern, M. Godfrey, 1966 .

Theory of Localized Contributions to the Chemical Shift. Application to Fluorobenzenes

T. P. Das, M. Karplus, 1961 .

Theory of Carbon NMR Chemical Shifts in Conjugated Molecules

Martin Karplus, M. Karplus, J. Pople, 1963 .

ELECTRONIC STRUCTURE OF THE MOLYBDENUM-IRON-SULFUR CLUSTER MOFE3S4(SH)63-ION

M. Karplus, M. Cook, 1985 .

Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

M. Karplus, H. V. van Vlijmen, S. Curry, 1998, Journal of molecular biology.

Ab initio studies of polyenes. I. 1,3‐butadiene

M. Karplus, Hong Guo, 1991 .

Basis set and polarization function effects on optimized geometries and harmonic frequencies at the second‐order Mo/ller–Plesset perturbation level

M. Karplus, Hong Guo, 1989 .

Vibrational approach to the dynamics of an α‐helix

Ronald M. Levy, Martin Karplus, M. Karplus, 1979 .

Dyanmics of organic reactions

M. Karplus, I. S. Y. Wang, M. Karplus, 1973 .

Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy.

M Karplus, M. Karplus, B. Roux, 1995, Biophysical journal.

Molecular dynamics simulations of the gramicidin channel.

M Karplus, M. Karplus, B. Roux, 1994, Annual review of biophysics and biomolecular structure.

Ion transport in a model gramicidin channel. Structure and thermodynamics.

M Karplus, M. Karplus, B. Roux, 1991, Biophysical journal.

Pathways for conformational interconversion of calix[4]arenes

M. Karplus, D. Reinhoudt, Stefan Fischer, 1995 .

Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect

Martin Karplus, M. Karplus, Hong Guo, 1994 .

Theoretical study of the ground and excited singlet states of styrene

M. Karplus, V. Vaida, R. Hemley, 1985 .

The calorimetric criterion for a two‐state process revisited

Yaoqi Zhou, Martin Karplus, M. Karplus, 1999, Protein science : a publication of the Protein Society.

Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization

Martin Karplus, M. Karplus, A. Warshel, 1972 .

Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study.

M. Karplus, T. Ichiye, 1983, Biochemistry.

Molecular dynamics simulation of the proline conformational equilibrium and dynamics in antamanide using the CHARMM force field

Roland L. Dunbrack, Richard R. Ernst, Martin Karplus, 1993 .

Calculation of one‐electron properties of LiH from Xα multiple‐scattering wave functions

M. Karplus, M. Cook, 1980 .

The calculation of one-electron properties from Xα multiple scattering wavefunctions

M. Karplus, D. Case, 1976 .

NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models

Ronald M. Levy, Peter G. Wolynes, Martin Karplus, 1981 .

Electronic structure of icosahedral cobalt-sulfur clusters

M. Karplus, J. Bashkin, G. Hoffman, 1990 .

Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers

Martin Karplus, M. Karplus, Hong Guo, 1992 .

Phosphate ester hydrolysis: calculation of gas-phase reaction paths and solvation effects

M. Karplus, Xiaoling Liang, A. Dejaegere, 1994 .

Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis.

M. Karplus, A. Golosov, 2007, The journal of physical chemistry. B.

Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin : ligand dynamics in the first 10 ps

M. Karplus, J. Straub, 1991 .

On the origin of a low-lying forbidden transition in polyenes and related molecules

Klaus Schulten, Martin Karplus, M. Karplus, 1972 .

Vibrational analysis of the lowest 1B+u state of trans,trans 1,3,5,7‐octatetraenea)

M. Karplus, R. Hemley, T. A. Spiglanin, 1984 .

Photodynamics of polyenes: The effect of electron correlation on potential surfaces

M. Karplus, A. Lasaga, R. J. Aerni, 1980 .

Guanidinium as a Probe of the Gramicidin Channel Interior

M. Karplus, M. Pear, D. Busath, 1988 .

The Inductive Effect in the Toluene Anion Radical

M. Karplus, D. Lazdins, 1965 .

Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition

Andrej Sali, Eugene I. Shakhnovich, Martin Karplus, 1998 .

How does a protein fold?

M. Karplus, E. Shakhnovich, A. S˘ali, 1994, Nature.

Spin dependent properties of perturbed wave functions: An analytic comparison of the exact, UHF, and spin-projected UHF states

M. Karplus, P. Rossky, 1980 .

Active site dynamics of acyl‐chymotrypsin

M. Karplus, S. Nakagawa, Hsiang‐Ai Yu, 1993, Proteins.

Spin Delocalization in the Allyl and Ethyl Radicals

M. Karplus, D. Lazdins, 1966 .

Deuterium Isotope Effects in the Electron Spin Resonance Spectra of Naphthalene Negative Ions

M. Karplus, J. Bolton, R. Lawler, 1967 .

Comment on the Interpretation of Hyperconjugation and Spin Delocalization in Organic Radicals

M. Karplus, J. Colpa, E. D. Boer, 1967 .

Gaussian‐Transform Method for Molecular Integrals. I. Formulation for Energy Integrals

Martin Karplus, M. Karplus, I. Shavitt, 1965 .

Analysis of Charge Distributions: Hydrogen Fluoride

M. Karplus, C. W. Kern, 1964 .

Nuclear Quadrupole Coupling in Polyatomic Molecules

M. Karplus, C. W. Kern, 1965 .

ELECTRON SPIN RESONANCE STUDIES OF DEUTERIUM ISOTOPE EFFECTS. A NOVEL RESONANCE-INTEGRAL PERTURBATION

M. Karplus, R. Lawler, G. Fraenkel, 1965 .

Ion Radicals of Methyl‐Substituted Benzenes: Temperature Dependence of Spin and Charge Densities

M. Karplus, T. H. Brown, 1963 .

Analysis of the interaction of organic phosphates with hemoglobin.

M. Karplus, A. Szabó, 1976, Biochemistry.

The potential of mean force surface for the alanine dipeptide in aqueous solution: a theoretical approach

Bernard Pettitt, Martin Karplus, M. Karplus, 1985 .

Perturbation theory and ionic models for alkali halide systems. I Diatomics

M. Karplus, P. Brumer, 1973 .

Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis

Bruce Tidor, Jiali Gao, Martin Karplus, 1991 .

The dynamic picture of protein structure

J. Andrew McCammon, Martin Karplus, M. Karplus, 1983 .

A molecular dynamics analysis of protein structural elements

M Karplus, C M Dobson, M. Karplus, 1989, Proteins.

T Cell Recognition of Hapten

M Karplus, M. Karplus, O. Michielin, 1999, The Journal of Biological Chemistry.

The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.

Martin Karplus, M. Karplus, L. Beese, 2010, Structure.

DNA polymorphism: a comparison of force fields for nucleic acids.

Martin Karplus, M. Karplus, Swarnalatha Y Reddy, 2003, Biophysical journal.

Renormalized configuration interaction method for electron correlation in the excited states of polyenes

Klaus Schulten, Martin Karplus, M. Karplus, 1978 .

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

Harmonic analysis of large systems. I. Methodology

Dusanka Janezic, Bernard R. Brooks, Martin Karplus, 1995, J. Comput. Chem..

The Water Molecule

M. Karplus, C. W. Kern, 1972 .

Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules.

M. Karplus, A. Warshel, 1974, Journal of the American Chemical Society.

Approximate Self-Consistent-Field Study of the (NiF 6 ) 4- Cluster

M. Karplus, B. Kleinman, 1971 .

Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application.

M. Karplus, R. Sauer, D. Patel, 1984, Proceedings of the National Academy of Sciences of the United States of America.

A method for determining reaction paths in large molecules: application to myoglobin

Ron Elber, Martin Karplus, M. Karplus, 1987 .

A mathematical model for structure-function relationships in hemoglobin.

M. Karplus, A. Szabó, Attila Szabo, 1972, Biochemical and biophysical research communications.

[15]Internal dynamics of proteins

Martin Karplus, M. Karplus, 1986 .

The internal dynamics of globular proteins.

M Karplus, J A McCammon, M. Karplus, 1981, CRC critical reviews in biochemistry.

Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode.

M Karplus, M. Karplus, H. Eklund, 1979, The Journal of biological chemistry.

Effective coupling in biological electron transfer: exponential or complex distance dependence?

M. Karplus, J. Evenson, 1993, Science.

Kinetics of diffusion‐influenced bimolecular reactions in solution. II. Effects of the gating mode and orientation‐dependent reactivity

M. Karplus, Sangyoub Lee, 1987 .

Theoretical approaches to solvation of biopolymers.

M Karplus, C L Brooks, M. Karplus, 1986, Methods in enzymology.

Correlation effects in the spectra of polyenes

Klaus Schulten, Martin Karplus, M. Karplus, 1976 .

Equilibrium geometry and dynamics of the valence excited states of 1,3-butadiene

M. Karplus, R. Hemley, U. Dinur, 1983 .

CALCULATION OF PI,PI(*) EXCITED STATE CONFORMATIONS AND VIBRONIC STRUCTURE OF RETINAL AND RELATED MOLECULES

M. Karplus, A. Warshel, 1974 .

Implications of Torsional Potential of Retinal Isomers for Visual Excitation

M. Karplus, B. Honig, 1971, Nature.

Ring orientation in -ionone and retinals.

M. Karplus, B. Honig, B. Sykes, 1971, Proceedings of the National Academy of Sciences of the United States of America.

Correlation effects in the excited states of polydiacetylene models

M. Karplus, U. Dinur, 1982 .

Possible influence of a low-lying "covalent" excited state on the absorption spectrum and photoisomerization of 11-cis retinal

M. Karplus, K. Schulten, R. Birge, 1975 .

The singlet states of styrene. Theoretical vibrational analysis of the ultraviolet spectrum

M. Karplus, V. Vaida, R. Hemley, 1985 .

New sum rules for electronic absorption spectra

M. Karplus, R. Coalson, 1984 .

Generalized quantum Liouville equation: Its solution by wave packet dynamics

Martin Karplus, Rob D. Coalson, M. Karplus, 1983 .

Theoretical studies of the visual chromophore

M. Karplus, B. Honig, A. Warshel, 1975 .

Semiclassical trajectory approach to photoisomerization

M. Karplus, A. Warshel, 1975 .

Theory of Retinal and Related Molecules

M. Karplus, 1973 .

Vibrational structure of electronic transitions in conjugated molecules

M. Karplus, A. Warshel, 1972 .

Spinach on the Ceiling

M. Karplus, 2020 .

Development of Multiscale Models for Complex Chemical Systems: From H + H2 to Biomolecules (Nobel Lecture)

Martin Karplus, M. Karplus, 2014 .

Molecular Dynamics Simulations of Proteins

M. Karplus, 1987 .

Dynamical theory of activated processes in globular proteins.

M Karplus, J A McCammon, M. Karplus, 1982, Proceedings of the National Academy of Sciences of the United States of America.

Dynamics of activated processes in globular proteins.

M. Karplus, J. Mccammon, 1979, Proceedings of the National Academy of Sciences of the United States of America.

A model for the simulation of an aqueous dipeptide solution

M. Karplus, P. Rossky, A. Rahman, 1979 .

Mechanism of tertiary structural change in hemoglobin.

M Karplus, M. Karplus, B. Gelin, 1977, Proceedings of the National Academy of Sciences of the United States of America.

Interpretation of the binding of carbon monoxide to hemoglobin under photodissociating conditions.

M. Karplus, A. Szabó, 1973, Proceedings of the National Academy of Sciences of the United States of America.

Collision Dynamics and the Statistical Theories of Chemical Reactions. II. Comparison of Reaction Probabilities

M. Karplus, K. Morokuma, 1971 .

Electronic structure of cyanide complexes of hemes and heme proteins.

M. Karplus, R. Shulman, S. Glarum, 1971, Journal of molecular biology.

Collision Dynamics and the Statistical Theories of Chemical Reactions. I. Average Cross Section from Transition‐State Theory

M. Karplus, K. Morokuma, B. Eu, 1969 .

Spin Delocalization and Vibrational–Electronic Interaction in the Toluene Ion–Radicals

M. Karplus, D. Purins, 1969 .

Perturbed Hartree–Fock Theory. I. Diagrammatic Double‐Perturbation Analysis

M. Karplus, T. Caves, 1969 .

Quasiclassical Trajectory Analysis for the Reaction of Potassium Atoms with Oriented Methyl Iodide Molecules1

M. Karplus, M. Godfrey, 1966 .

Dynamics of Reactive Collisions: The H +H2 Exchange Reaction

Martin Karplus, R. N. Porter, M. Karplus, 1964 .

Potential-Energy Surface for H 3

M. Karplus, I. Shavitt, F. Minn, 1964 .

Sidechain Torsional Potentials and Motion of Amino Acids in Proteins : Bovine Pancreatic Trypsin Inhibitor ( nuclear magnetic resonance of proteins / theory of protein structure / energy functions applied to proteins / sidechain rotation rates / conformational potentials )

M. Karplus, B. Gelin, 2022 .

Valence‐Bond Interpretation of Electron Coupled Proton‐Proton Magnetic Interactions Measured via Deuterium Substitution

H. S. Gutowsky, M. Karplus, D. H. Anderson, 1957 .

Molecular dynamics: applications to proteins.

M. Karplus, John Kuriyan, Axel T. Brunger, 1987, Cold Spring Harbor symposia on quantitative biology.

Molecular Dynamics of Biomolecules: Overview and Applications

M. Karplus, 1986 .

Molecular Dynamics of Proteins

M. Karplus, 1986 .

Molecular dynamics: applications to proteins.

M Karplus, M. Karplus, 1986, Annals of the New York Academy of Sciences.

Excitation operators and the extended random phase approximation: II. Applications

M. Karplus, A. Lasaga, 1979 .

Theoretical analysis of the 11Bu+ (1B1+) .rarw. 11Ag- (1A1-) transition of trans- and cis-1,3,5-hexatriene

M. Karplus, V. Vaida, R. Hemley, 1988 .

Reprint of: Semiclassical trajectory approach to photoisomerization

M. Karplus, A. Warshel, 2013 .

THEORY OF PROTON COUPLING CONSTANTS IN UNSATURATED MOLECULES

M. Karplus, 1960 .

Weak Interactions in Molecular Quantum Mechanics

M. Karplus, 1960 .

Conformational Properties of the Delta Opioid Peptide Cyclic(D-Pen2,D-Pen5)enkephalin in Aqueous Solution Determined by NMR and Energy Minimization Calculations.

M. Karplus, V. Hruby, B. Pettitt, 1988 .

The conformational properties of the delta opioid peptide [D-Pen2,D-Pen5]enkephalin in aqueous solution determined by NMR and energy minimization calculations

B. Montgomery Pettitt, Victor J. Hruby, Martin Karplus, 1988 .

Kinetics of diffusion‐influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions

M. Karplus, Sangyoub Lee, 1987 .

Dynamics of DNA oligomers.

M Karplus, B Tidor, M. Karplus, 1983, Journal of biomolecular structure & dynamics.

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

Stuart L. Schreiber, Gregory A. Weiss, Erik Evensen, 2007, J. Comput. Aided Mol. Des..

Thermodynamics and kinetic analysis of F0F1-ATPase

M. Karplus, Y. Gao, Wei Yang, 2006 .

A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase

Wei Yang, Martin Karplus, Yi Qin Gao, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment.

M Karplus, M. Karplus, B. Gelin, 1979, Biochemistry.

Molecular dynamics simulations of disulfide cross-linked DNA decamers

M. Karplus, J. Wiórkiewicz-Kuczera, A. E. Ferentz, 1993 .

Multicenter Integrals in Molecular Quantum Mechanics

Martin Karplus, M. Karplus, I. Shavitt, 1962 .

Product-assisted catalysis in base-excision DNA repair

J. Christopher Fromme, M. Karplus, Wei Yang, 2003, Nature Structural Biology.

Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues.

Vincent Zoete, Nicolas Winssinger, Martin Karplus, 2005, Journal of the American Chemical Society.

Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP—substrate complex

M. Karplus, A. Caflisch, S. Fischer, 1997 .

Test of the closed-shell overlap-repulsion model for the ethane barrier

M. Karplus, R. M. Stevens, 1972 .

An integral equation theory study of the solvent-induced reaction barrier in the nucleophilic addition of hydroxide to formaldehyde

Martin Karplus, M. Karplus, Hsiang Ai. Yu, 1990 .

A thermodynamic analysis of solvation

Martin Karplus, M. Karplus, Hsiang‐Ai Yu, 1988 .

Conformational sampling using high‐temperature molecular dynamics

M. Karplus, R. Bruccoleri, 1990, Biopolymers.

Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin.

M Karplus, A M Gronenborn, G M Clore, 1986, Journal of molecular biology.

Constrained Molecular Wavefunctions: HF Molecule

M. Karplus, A. Mukherji, 1963 .

Magnetic Properties of Hydrogen Fluoride. I. Rotational Moment

T. P. Das, M. Karplus, 1962 .

Magnetic Interactions in Lithium Hydride

M. Karplus, H. Kolker, 1961 .

Aspects of Time-Dependent Perturbation Theory

P. W. Langhoff, M. Karplus, S. Epstein, 1972 .

Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase.

Martin Karplus, Qiang Cui, M. Karplus, 2003, Advances in protein chemistry.

NUCLEAR QUADRUPOLE INTERACTIONS IN ALKALI HALIDE MOLECULES

T. P. Das, M. Karplus, 1959 .

A Variation‐Perturbation Approach to the Interaction of Radiation with Atoms and Molecules

M. Karplus, H. Kolker, 1963 .

Molecular basis for the Born model of ion solvation

Benoît Roux, Martin Karplus, M. Karplus, 1990 .

Deuteron Quadrupole Coupling Constant in CH3D

M. Karplus, T. Caves, 1966 .

NONEQUILIBRIUM CONTRIBUTION TO THE RATE OF REACTION. III. ISOTHERMAL MULTICOMPONENT SYSTEMS.

M. Karplus, B. Shizgal, 1971 .

Nonequilibrium Contributions to the Rate of Reaction. I. Perturbation of the Velocity Distribution Function

M. Karplus, B. Shizgal, 1970 .

Small-world view of the amino acids that play a key role in protein folding.

M Karplus, M Vendruscolo, N V Dokholyan, 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

Three-dimensional "Pople diagram"

M. Karplus, 1990 .

Construction of a model for the three-dimensional structure of human renal renin.

M Karplus, M. Karplus, E. Haber, 1985, Hypertension.

Symmetric H3: A Semiempirical and Ab Initio Study of a Simple Jahn–Teller System

M. Karplus, R. Porter, R. M. Stevens, 1968 .

The fundamentals of protein folding: bringing together theory and experiment.

M Karplus, C M Dobson, M. Karplus, 1999, Current opinion in structural biology.

Nonequilibrium Contributions to the Rate of Reactions. II. Isolated Multicomponent Systems

Bernie D. Shizgal, Martin Karplus, M. Karplus, 1971 .

Theoretical studies of H+H2 reactive scattering

M. Karplus, G. Wolken, 1974 .

PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis

Martin Karplus, Nancy Kleckner, M. Karplus, 2010, Proceedings of the National Academy of Sciences.

Potential energy function for cation–peptide interactions: An ab initio study

Benoît Roux, Martin Karplus, M. Karplus, 1995, J. Comput. Chem..

PRUEFUNG DES ′CLOSED-SHELL OVERLAP-REPULSION′-MODELLS FUER DIE ROTATIONSBARRIERE IN AETHAN

M. Karplus, R. M. Stevens, 1972 .

Theoretical studies on the hydrolysis of phosphate diesters in the gas phase, solution, and RNase A

M. Karplus, D. York, X. López, 2002 .

Inelastic neutron scattering analysis of low-frequency motions in proteins : harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor

Bruce Tidor, Martin Karplus, Jeremy C. Smith, 1990 .

Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor

Bernard R. Brooks, Martin Karplus, Jeremy C. Smith, 1986 .

Molecular dynamics of an a-helical polypeptide: Temperature dependence and deviation from harmonic behavior (protein dynamics/temperature factor/quantum corrections/fluctuations/normal modes)

Ronald M. Levy, David Perahia, Martin Karplus, 1982 .

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase.

Jianpeng Ma, Martin Karplus, Qiang Cui, 2002, Structure.

Structural details of urea binding to barnase: a molecular dynamics analysis.

A Caflisch, M Karplus, M. Karplus, 1999, Structure.

New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.

Amedeo Caflisch, Martin Karplus, M. Karplus, 2013, The journal of physical chemistry. B.

Molecular dynamics simulations of biomolecules

Jeremy M. Berg, J. Berg, M. Karplus, 2002, Nature Structural Biology.

Comparisons of Dispersion Force Bounding Methods with Applications to Anisotropic Interactions

P. W. Langhoff, M. Karplus, R. Gordon, 1971 .

Van der Waals Forces in Atoms and Molecules

M. Karplus, H. Kolker, 1964 .

Vicinal coupling constants and protein dynamics.

M. Karplus, J. Hoch, C. Dobson, 1985, Biochemistry.

Padé Approximants for Two‐ and Three‐Body Dipole Dispersion Interactions

P. W. Langhoff, M. Karplus, 1970 .

Upper Bounds on Many-Channel Scattering Phase Shifts by an Adiabatic-Type Approximation

M. Karplus, R. Gerber, 1969 .

Conformations of intermediates in the folding of the pancreatic trypsin inhibitor.

M Karplus, D J States, C M Dobson, 1987, Journal of molecular biology.

A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain

John Kuriyan, Martin Karplus, Michael A. Koldobskiy, 2006, PLoS biology.

Model for the structure of the lipid bilayer.

R M Venable, M Karplus, M. Karplus, 1991, Proceedings of the National Academy of Sciences of the United States of America.

The effect of maternal measles on the fetus.

M. Karplus, I. Sarov, E. Gazala, 1985, Pediatric infectious disease.

Protein folding dynamics: The diffusion‐collision model and experimental data

M Karplus, D L Weaver, M. Karplus, 1994, Protein science : a publication of the Protein Society.

Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: assignment of aromatic resonances with application to protein folding, structure, and dynamics.

M. Karplus, E. O’Shea, D. Nguyen, 1989, Biochemistry.

Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism

M. Karplus, K. Nam, J. Pu, 2014, Proceedings of the National Academy of Sciences.

How subunit coupling produces the γ-subunit rotary motion in F1-ATPase

Martin Karplus, Jingzhi Pu, M. Karplus, 2008, Proceedings of the National Academy of Sciences.

Structure of the EmrE multidrug transporter and its use for inhibitor peptide design

M. Karplus, C. Deber, V. Ovchinnikov, 2018, Proceedings of the National Academy of Sciences.

Absolute Binding Free Energies: A Quantitative Approach for Their Calculation

Stefan Boresch, Martin Karplus, M. Karplus, 2003 .

Thermodynamics of protein folding: a microscopic view.

Themis Lazaridis, Martin Karplus, M. Karplus, 2002, Biophysical chemistry.

Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI.

M. Karplus, J. Mccammon, B. Gelin, 1980, Biophysical journal.

Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations.

M. Karplus, I. Andricioaei, D. Herschbach, 2004, Biophysical journal.

Thermal expansion of a protein.

I. Kuntz, M. Karplus, G. Petsko, 1987, Biochemistry.

Brownian dynamics simulation of protein folding: A study of the diffusion‐collision model

M. Karplus, D. Bashford, Sangyoub Lee, 1987, Biopolymers.

Picosecond dynamics of tyrosine side chains in proteins.

M Karplus, J A McCammon, P G Wolynes, 1979, Biochemistry.

Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase

Martin Karplus, Qiang Cui, M. Karplus, 2003 .

X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution.

M Karplus, J Kuriyan, G A Petsko, 1986, Journal of molecular biology.

First Passage Analysis of the Folding of a β-Sheet Miniprotein: Is it More Realistic Than the Standard Equilibrium Approach?

M. Karplus, I. Kalgin, S. Chekmarev, 2014, The journal of physical chemistry. B.

Neural networks for protein structure prediction.

M Karplus, M. Karplus, L. Holley, 1991, Methods in enzymology.

Molecular and stochastic dynamics of proteins.

M Karplus, K Schulten, W Nadler, 1987, Proceedings of the National Academy of Sciences of the United States of America.

Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin.

M Karplus, A M Gronenborn, G M Clore, 1986, Proceedings of the National Academy of Sciences of the United States of America.

The importance of larger data sets for protein secondary structure prediction with neural networks

J M Chandonia, M Karplus, M. Karplus, 1996, Protein science : a publication of the Protein Society.

Protein sidechain conformer prediction: a test of the energy function.

M Karplus, M. Karplus, T. Lazaridis, 1998, Folding & design.

Computer simulations of the OmpF porin from the outer membrane of Escherichia coli.

M. Karplus, M. Watanabe, Tilman Schirmer, 1997, Biophysical journal.

The Levinthal paradox: yesterday and today.

M Karplus, M. Karplus, 1997, Folding & design.

Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2.

M Karplus, A M Gronenborn, G M Clore, 1986, Journal of molecular biology.

Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H nuclear magnetic resonance and restrained molecular dynamics.

M Karplus, A M Gronenborn, G M Clore, 1985, Journal of molecular biology.

Protein structural transitions and their functional role

Jianpeng Ma, Wei Yang, Martin Karplus, 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

The contribution of cross‐links to protein stability: A normal mode analysis of the configurational entropy of the native state

M Karplus, B Tidor, M. Karplus, 1993, Proteins.

A conformational isomer of bovine pancreatic trypsin inhibitor protein produced by refolding

M. Karplus, D. States, C. Dobson, 1980, Nature.

Translocation mechanism of long sugar chains across the maltoporin membrane channel.

Stefan Fischer, Martin Karplus, M. Karplus, 2002, Structure.

Crystal Structures of Two Closely Related but Antigenically Distinct HLA-A2/Melanocyte-Melanoma Tumor-Antigen Peptide Complexes1

M. Karplus, D. Wiley, P. Romero, 2001, The Journal of Immunology.

Tumor-Antigen Peptide Complexes HLA-A 2 / Melanocyte-Melanoma Antigenically Distinct Crystal Structures of Two Closely Related but C

M. Karplus, D. Wiley, P. Romero, 2001 .

Solution NMR studies of intact lambda repressor.

M Karplus, M. Karplus, R. Sauer, 1983, Journal of biomolecular structure & dynamics.

Forces and energetics of hapten-antibody dissociation: a biased molecular dynamics simulation study.

A Caflisch, M Karplus, E Paci, 2001, Journal of molecular biology.

Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis.

Olivier Michielin, Martin Karplus, M. Karplus, 2002, Journal of molecular biology.

The dynamics of proteins.

M. Karplus, J. Mccammon, J. McCammon, 1982, Scientific American.

The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

M Karplus, M. Karplus, S Boresch, 1995, Journal of molecular biology.

Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning

Martin Karplus, Simone Conti, M. Karplus, 2019, PLoS Comput. Biol..

A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance

M. Karplus, V. Ovchinnikov, 2022, Frontiers in Immunology.

Simulations of lysozyme: internal motions and the reaction mechanism.

M. Karplus, C. Post, M. Karplus, 1996, EXS.

Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis.

M. Karplus, T. Ichiye, 1988, Biochemistry.

Structure and internal mobility of proteins: A molecular dynamics study of hen egg white lysozyme

M. Karplus, B. D. Olafson, S. Swaminathan, 1986, Biopolymers.

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations.

M. Karplus, B. Brooks, C. Dobson, 1986, Journal of molecular biology.

What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.

Jane Clarke, Robert B Best, Martin Karplus, 2005, Journal of molecular biology.

Dynamics simulation studies of apoazurin of Alcaligenes denitrificans

M. Karplus, D. Nguyen, G. Fleming, 1988 .

A simulation based model of NMR T1 relaxation in lipid bilayer vesicles

Martin Karplus, Richard W. Pastor, Richard M. Venable, 1988 .

Comments on the Signs of Proton Coupling Constants

M. Karplus, 1962 .

Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

M. Karplus, M. Meuwly, P. Gupta, 2018, eLife.

Modeling of side chains, loops, and insertions in proteins.

M Karplus, M. Karplus, N. Summers, 1991, Methods in enzymology.

Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations.

M Karplus, M. Karplus, N. Summers, 1990, Journal of molecular biology.

Time dependence of atomic fluctuations in proteins: analysis of local and collective motions in bovine pancreatic trypsin inhibitor.

M Karplus, M. Karplus, S. Swaminathan, 1982, Biochemistry.

Molecular Dynamics Studies of Protein and Peptide Folding and Unfolding

Amedeo Caflisch, Martin Karplus, M. Karplus, 1994 .

Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach

M. Karplus, C. Brooks, A. Brünger, 1985, Biopolymers.

Local and collective motions in protein dynamics.

M. Karplus, S. Swaminathan, W. V. van Gunsteren, 2008, Ciba Foundation symposium.

Dynamics of Peptides and Proteins

M. Karplus, 1982 .

ASPECTS OF PROTEIN DYNAMICS *

M. Karplus, 1981, Annals of the New York Academy of Sciences.

Heat capacity and compactness of denatured proteins.

M Karplus, M. Karplus, T. Lazaridis, 1999, Biophysical chemistry.

Configurational entropy of native proteins.

M Karplus, B M Pettitt, M. Karplus, 1987, Biophysical journal.

Protein dynamics investigated by inherent structure analysis

Francesco Rao, Martin Karplus, M. Karplus, 2010, Proceedings of the National Academy of Sciences.

Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase.

M. Karplus, S. Wodak, B. Tidor, 1991, Ciba Foundation symposium.

Free energy simulations: The meaning of the individual contributions from a component analysis

M Karplus, M. Karplus, G. Archontis, 1994, Proteins.

Proton and nitrogen sequential assignments and secondary structure determination of the human FK506 and rapamycin binding protein.

M. Karplus, S. Schreiber, S. Michnick, 1991, Biochemistry.

Insights into the origin of the high energy-conversion efficiency of F1-ATPase

M. Karplus, K. Nam, 2019, Proceedings of the National Academy of Sciences.

How Biomolecular Motors Work: Synergy Between Single Molecule Experiments and Single Molecule Simulations

M. Karplus, J. Pu, 2010 .

A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1-ATPase

Wei Yang, Martin Karplus, Yi Qin Gao, 2005, Cell.

The missing link between thermodynamics and structure in F1-ATPase

M Karplus, M. Karplus, Jianpeng Ma, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Diffusion‐collision model for the folding kinetics of myoglobin

I. Kuntz, M. Karplus, F. Cohen, 1988, Proteins.

Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.

Victor Ovchinnikov, Martin Karplus, M. Karplus, 2012, The journal of physical chemistry. B.

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.

Victor Ovchinnikov, Martin Karplus, M. Karplus, 2014, The Journal of chemical physics.

The role of carbon‐donor hydrogen bonds in stabilizing tryptophan conformations

M. Karplus, R. Petrella, 2004, Proteins.

Solution of a Protein Crystal Structure with a Model Obtained from NMR Interproton Distance Restraints

M. Karplus, G. Petsko, A. Gronenborn, 1987, Science.

Functionality map analysis of the active site cleft of human thrombin

M Karplus, P D Grootenhuis, M. Karplus, 1996, J. Comput. Aided Mol. Des..

Determining the conformational change that accompanies donor-acceptor distance fluctuations: an umbrella sampling analysis.

M. Karplus, G. Luo, 2011, The journal of physical chemistry. B.

Calculation of free-energy differences by confinement simulations. Application to peptide conformers.

M Karplus, M. Karplus, M. Cecchini, 2009, The journal of physical chemistry. B.

Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors

M. Karplus, J. Changeux, P. Corringer, 2006, Proceedings of the National Academy of Sciences.

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

M Karplus, B Tidor, M. Karplus, 1994, Journal of molecular biology.

Internal dynamics of proteins.

M. Karplus, 1986, Methods in Enzymology.

Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment.

S Cusack, M Karplus, B Tidor, 1988, Journal of molecular biology.

Diffusive reaction dynamics on invariant free energy profiles

Sergei V Krivov, Martin Karplus, M. Karplus, 2008, Proceedings of the National Academy of Sciences.

Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: A study of models and realistic systems

M. Karplus, Q. Cui, 2002 .

BRIEF COMMUNICATION CONFIGURATIONAL ENTROPY OF NATIVE PROTEINS

M. Karplus, T. Ichiye, B. M. PErTIrr, 2005 .

Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.

M Karplus, M. Karplus, J. Ma, 1997, Proceedings of the National Academy of Sciences of the United States of America.

Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations

Martin Karplus, Qiang Cui, M. Karplus, 2000 .

Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism

M. Karplus, W. Lipscomb, Q. Cui, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Lack of limb motor asymmetry in the neonate.

M. Karplus, A. Korczyn, J. Sage, 1978, Journal of neurobiology.

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence.

Wei Yang, Martin Karplus, M. Karplus, 2004, The Journal of chemical physics.

Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into the catalytic mechanism.

M. Karplus, K. Nam, G. Verdine, 2009, Journal of the American Chemical Society.

New methods for accurate prediction of protein secondary structure

J M Chandonia, M Karplus, M. Karplus, 1999, Proteins.

Force generation in kinesin hinges on cover-neck bundle formation.

Martin Karplus, Wonmuk Hwang, Matthew J Lang, 2008, Structure.

Kinesin's cover-neck bundle folds forward to generate force

Ahmad S. Khalil, Angela M. Belcher, Martin Karplus, 2008, Proceedings of the National Academy of Sciences.

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV

M. Karplus, A. Chakraborty, V. Ovchinnikov, 2021, bioRxiv.

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis.

M Karplus, M. Karplus, J. Ma, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Modeling zinc in biomolecules with the self consistent charge‐density functional tight binding (SCC‐DFTB) method: Applications to structural and energetic analysis

Thomas Frauenheim, Qiang Cui, Efthimios Kaxiras, 2003, J. Comput. Chem..

Vibrational vs. translational activation in the H2,H2 and H2,D2 exchange reactions

M. Karplus, K. Morokuma, L. Pedersen, 1967 .

Convergence of the valence-bond calculation for methane

Martin Karplus, M. Karplus, M. Raimondi, 1977 .

Isotope effect on the hyperfine splittings of the deuteriobenzene anions: An example of the dynamic Jahn–Teller effect

M. Karplus, D. Purins, 1975 .

Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase.

S J Wodak, M Karplus, B Tidor, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Brownian dynamics simulation of a lipid chain in a membrane bilayer

Martin Karplus, Richard W. Pastor, Richard M. Venable, 1988 .

The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

M. Karplus, Yaoqi Zhou, R. Berry, 2002 .

Magnetic Susceptibility of Diatomic Molecules

M. Karplus, H. Kolker, 1963 .

Theory of Nuclear Magnetic Shielding in Diatomic Molecules

M. Karplus, H. Kolker, 1964 .

Chemical Shifts in Xenon Fluorides

M. Karplus, C. W. Kern, D. Lazdins, 1963 .

The elastic properties of the structurally characterized myosin II S2 subdomain: a molecular dynamics and normal mode analysis.

Martin Karplus, Srboljub M. Mijailovich, M. Karplus, 2008, Biophysical journal.

Dynamics of molecules with internal degrees of freedom by multiple time-step methods

Masakatsu Watanabe, Martin Karplus, M. Karplus, 1993 .

Molecular dynamics simulations of biomolecules.

M. Karplus, J. Mccammon, J. McCammon, 2002, Nature structural biology.

Internal motion of proteins: nuclear magnetic resonance measurements and dynamic simulations.

M. Karplus, C. Dobson, 1986, Methods in enzymology.

Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme

M. Karplus, C. Dobson, R. Levy, 1984 .

New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities

Arnaud Blondel, Martin Karplus, M. Karplus, 1996, J. Comput. Chem..

Quantum Theory of (H, H2) Scattering: Two‐Body Potential and Elastic Scattering

M. Karplus, K. Tang, 1968 .

Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1*

Peter S. Kutchukian, M. Karplus, B. R. Bowman, 2012, The Journal of Biological Chemistry.

Harmonic analysis of large systems. III. Comparison with molecular dynamics

Dusanka Janezic, Martin Karplus, Richard M. Venable, 1995, J. Comput. Chem..

Genetic Methods in High-Resolution NMR Studies of Proteins

M. Karplus, R. Sauer, N. Fischbein, 1986 .

Hemoglobin Bohr effects: atomic origin of the histidine residue contributions.

M. Karplus, M. Schaefer, G. Zheng, 2013, Biochemistry.

Unsuspected pathway of the allosteric transition in hemoglobin

M. Karplus, Stefan Fischer, K. Nam, 2011, Proceedings of the National Academy of Sciences.

Self-consistent determination of the transition state for protein folding: Application to a fibronectin type III domain

M. Karplus, E. Paci, M. Vendruscolo, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Analysis of proton release in oxygen binding by hemoglobin: implications for the cooperative mechanism.

M. Karplus, A. W. Lee, C. Poyart, 1988, Biochemistry.

Simulation analysis of triose phosphate isomerase: conformational transition and catalysis.

M. Karplus, M. Field, J. Evanseck, 1992, Faraday discussions.

Computer simulation and analysis of the reaction pathway of triosephosphate isomerase.

M Karplus, G A Petsko, M. Karplus, 1991, Biochemistry.

Neural networks for secondary structure and structural class predictions

J M Chandonia, M Karplus, M. Karplus, 1995, Protein science : a publication of the Protein Society.

Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering.

Jane Clarke, Robert B Best, Emanuele Paci, 2002, Journal of molecular biology.

Protein structural fluctuations during a period of 100 ps

M. Karplus, J. Mccammon, M. KARPLUS, 1979, Nature.

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints.

M. Karplus, M. Martí-Renom, R. Stote, 1998, Journal of molecular biology.

Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant.

M. Karplus, F. Lau, 1994, Journal of molecular biology.

Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry.

Martin Karplus, Herman W T van Vlijmen, M. Karplus, 2005, Journal of molecular biology.

Strandwise translocation of a DNA glycosylase on undamaged DNA

M. C. Spong, Michael Ruogu Zhang, M. Karplus, 2012, Proceedings of the National Academy of Sciences.

Entrapment and Structure of an Extrahelical Guanine Attempting to Enter the Active Site of a Bacterial DNA Glycosylase, MutM*

M. C. Spong, M. Karplus, K. Nam, 2009, The Journal of Biological Chemistry.

Role of Active Site Residues and Solvation in RNase A

M. Karplus, C. Brooks, A. Brünger, 1986 .

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme

Gregory L. Verdine, M. C. Spong, Kwangho Nam, 2009, Nature.

Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange.

Michele Vendruscolo, Emanuele Paci, Martin Karplus, 2003, Journal of the American Chemical Society.

M. Karplus, J. Mccammon, R. Levy, 1981 .

PADE APPROXIMANTS TO THE NORMAL DISPERSION EXPANSION OF DYNAMIC POLARIZABILITIES.

Martin Karplus, P. W. Langhoff, M. Karplus, 1970 .

Padé-Approximant Calculation of the Nonretarded van der Waals Coefficients for Two and Three Helium Atoms

M. Karplus, K. Tang, 1968 .

1H NMR aromatic spectrum of the operator binding domain of the lambda repressor: resonance assignment with application to structure and dynamics.

M. Karplus, R. Sauer, M. Weiss, 1987, Biochemistry.

Proton NMR studies of the association and folding of glucagon in solution

M. Karplus, C. Dobson, Mark Wagman, 1980, FEBS letters.

Dynamic distance disorder in proteins is caused by trapping.

Guobin Luo, Ioan Andricioaei, Martin Karplus, 2006, The journal of physical chemistry. B.

Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules

M. Karplus, Q. Cui, 2000 .

A Smooth Solvation Potential Based on the Conductor-Like Screening Model

Martin Karplus, M. Karplus, and Darrin M. York, 1999 .

Theoretical Studies of H + H2 Rotationally Inelastic Scattering

M. Karplus, W. Miller, G. Wolken, 1972 .

Relativistic Long‐Range Interactions between Atoms and Molecules

M. Karplus, T. Chang, 1970 .

Solvable Quantum‐Mechanical Model of Three‐Body Rearrangement Scattering

M. Karplus, K. Tang, B. Kleinman, 1969 .

A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors

Sung-Sau So, Martin Karplus, M. Karplus, 1999, J. Comput. Aided Mol. Des..

Free energy disconnectivity graphs: Application to peptide models

Sergei V. Krivov, Martin Karplus, M. Karplus, 2002 .

Multidimensional variational Gaussian wave packet dynamics with application to photodissociation spectroscopy

Martin Karplus, Rob D. Coalson, M. Karplus, 1990 .

The frequency-dependent polarizability of hydrogen-like atoms

M. Karplus, P. M. Getzin, 1972 .

Bounds for van der Waals Coefficients from Padé Approximants

P. W. Langhoff, M. Karplus, 1967 .

Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.

A Caflisch, M Karplus, M. Karplus, 1995, Journal of molecular biology.

Simulation of quantum systems using path integrals in a generalized ensemble

M. Karplus, I. Andricioaei, J. Straub, 2001 .

Theoretical investigations on Azotobacter vinelandii ferredoxin I: effects of electron transfer on protein dynamics.

Markus Meuwly, Martin Karplus, M. Karplus, 2004, Biophysical journal.

Simulation of proton transfer along ammonia wires: An “ab initio” and semiempirical density functional comparison of potentials and classical molecular dynamics

Markus Meuwly, Martin Karplus, M. Karplus, 2002 .

Gaussian-mixture umbrella sampling.

Martin Karplus, Paul Maragakis, M. Karplus, 2009, The journal of physical chemistry. B.

Shielding Anisotropies in Xenon Fluorides

M. Karplus, C. W. Kern, D. Lazdins, 1964 .

The potential of mean force between polyatomic molecules in polar molecular solvents

M. Karplus, B. Pettitt, 1985 .

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method.

Martin Karplus, Anders M N Niklasson, M. Karplus, 2011, The Journal of chemical physics.

The functional role of the hemoglobin-water interface.

M. Karplus, M. Meuwly, 2021, Molecular aspects of medicine.

Motions of an α‐helical polypeptide: Comparison of molecular and harmonic dynamics

Ronald M. Levy, David Perahia, M. Karplus, 1990 .

Electrostatic effects and hydrogen exchange behaviour in proteins. The pH dependence of exchange rates in lysozyme.

M. Karplus, D. States, C. Dobson, 1987, Journal of molecular biology.

Dipolar NMR relaxation of nonprotonated aromatic carbons in proteins. Structural and dynamical effects.

M. Karplus, C. Dobson, R. Levy, 1982, Biophysical journal.

Fluctuations and averaging of proton chemical shifts in the bovine pancreatic trypsin inhibitor.

M. Karplus, J. Hoch, C. Dobson, 1982, Biochemistry.

Effect of constraints, solvent and crystal environment on protein dynamics

M. Karplus, W. V. Gunsteren, 1981, Nature.

Pressure dependence of aromatic ring rotations in proteins: a collisional interpretation

M. Karplus, J. Mccammon, 1981 .

MOLECULAR DYNAMICS OF MYOGLOBIN AT 2980K Results from a 300-ps Computer Simulation

M. Karplus, R. Sheridan, R. Levy, 2005 .

Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy

Jeremy C. Smith, M. Karplus, J. Trewhella, 1986 .

Helix–coil transitions in a simple polypeptide model

Ronald M. Levy, J. A. McCammon, Martin Karplus, 1980 .

Dynamics of tyrosine ring rotations in a globular protein

J. A. McCammon, Martin Karplus, M. Karplus, 1980 .

Gaussian‐Transform Method for Molecular Integrals. II. Evaluation of Molecular Properties

Martin Karplus, M. Karplus, C. W. Kern, 1965 .

Charge Distribution in the Hydrogen Molecule

M. Karplus, 1956 .

Internal mobility of ferrocytochrome c

M. Karplus, J. Mccammon, T. Takano, 1980, Nature.

Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex

Amedeo Caflisch, Stefan Fischer, Martin Karplus, 1997, J. Comput. Chem..

Multicenter Pi‐Electron Integrals for the Benzene Molecule

Martin Karplus, M. Karplus, I. Shavitt, 1963 .

Theoretical investigations of Ferredoxin I: the possible role of internal water molecules on the coupled electron proton transfer reaction.

Markus Meuwly, Martin Karplus, M. Karplus, 2003, Faraday discussions.

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

Martin Karplus, M. Karplus, Christian Bartels† and, 1998 .

Dimerization of the operator binding domain of phage lambda repressor.

M Karplus, M. Karplus, R. Sauer, 1987, Biochemistry.

Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin.

Michiel J. M. Niesen, M. Karplus, M. Meuwly, 2020, The journal of physical chemistry. B.

Solvation thermodynamics: An approach from analytic temperature derivatives

Benoît Roux, Martin Karplus, M. Karplus, 1990 .

Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water.

M. Karplus, Hongyi Zhou, Yaoqi Zhou, 2003, Journal of molecular biology.

NO rebinding to myoglobin: a reactive molecular dynamics study.

Markus Meuwly, Martin Karplus, M. Karplus, 2002, Biophysical chemistry.

Unfolding proteins by external forces and temperature: the importance of topology and energetics.

M Karplus, E Paci, M. Karplus, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Molecular Recognition: An Example from Ligand Binding to Proteins

M. Karplus, F. Lau, 1994 .

Proton Spin Coupling by Pi Electrons: Correction and Comments

M. Karplus, 1969 .

The three‐dimensional structure of α1‐purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics

M Karplus, A M Gronenborn, G M Clore, 1986, The EMBO journal.

Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

Nathalie Reuter, Martin Karplus, M. Karplus, 2000 .

Two-metal-ion mechanism for hammerhead-ribozyme catalysis.

M. Karplus, F. Leclerc, 2006, The journal of physical chemistry. B.

Electrostatic contributions to molecular free energies in solution.

M. Karplus, H. V. van Vlijmen, M. Schaefer, 1998, Advances in protein chemistry.

Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis.

M. Karplus, D. Bashford, G. Canters, 1988, Journal of molecular biology.

Ab initio study of the vibrational spectra of N9-H and N7-H adenine and 9-methyladenine

Martin Karplus, M. Karplus, J. Wiórkiewicz-Kuczera, 1990 .

Pi release from myosin: a simulation analysis of possible pathways.

M. Karplus, M. Cecchini, Yuri Alexeev, 2010, Structure.

Stereochemistry of carbon monoxide binding to myoglobin and hemoglobin.

M. Karplus, D. Case, M. Karplus, 1978, Journal of molecular biology.

NATURE OF THE IRON-OXYGEN BOND IN OXYHEMOGLOBIN

M. Karplus, D. Case, B. H. Huynh, 1977 .

THE ROLE OF BONDED TERMS IN FREE ENERGY SIMULATIONS : 1. THEORETICAL ANALYSIS

Stefan Boresch, Martin Karplus, M. Karplus, 1999 .

Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach

Amedeo Caflisch, Martin Karplus, Hans J. Schramm, 2000, J. Comput. Aided Mol. Des..

Valence-bond approach to conservation of symmetry in concerted reactions

M. Karplus, D. Silver, 1975 .

Self-guided enhanced sampling methods for thermodynamic averages

M. Karplus, I. Andricioaei, A. Dinner, 2003 .

Extended wave packet dynamics; exact solution for collinear atom, diatomic molecule scattering

M. Karplus, R. Coalson, R. D. Coalson, 1982 .

Kinetic control of dimer structure formation in amyloid fibrillogenesis.

Roger D Kamm, Martin Karplus, Wonmuk Hwang, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Erratum: Analysis of Charge Distributions: Hydrogen Fluoride

M. Karplus, C. W. Kern, 1965 .

Model perturbation theoretic calculations with finite continuum basis sets

M. Karplus, P. Rossky, 1977 .

Dynamical search for bis-penicillamine enkephalin conformations.

M Karplus, B M Pettitt, V J Hruby, 1991, Biophysical journal.

Is protein unfolding the reverse of protein folding? A lattice simulation analysis.

M Karplus, M. Karplus, A. Dinner, 1999, Journal of molecular biology.

Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase.

A Caflisch, M Karplus, M. Karplus, 1994, Proceedings of the National Academy of Sciences of the United States of America.

Protein-Protein Interactions in DNA Recognition: 1H-NMR Studies of Lambda cI Repressors Genetically Altered by Site-Directed Mutagenesis

M. Karplus, R. Sauer, M. Weiss, 1986 .

Free Energy Simulations Come of Age: Protein—Ligand Recognition

Thomas Simonson, Martin Karplus, Georgios Archontis, 2002 .

Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference.

M Karplus, B Tidor, M. Karplus, 1985, Science.

Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations.

M. Karplus, W. Lipscomb, Q. Cui, 2003, Angewandte Chemie.

Simulation of Protein Dynamics

Martin Karplus, M. Karplus, A. McCammon, 1980 .

A POSITION DEPENDENT FRICTION MODEL FOR SOLUTION REACTIONS IN THE HIGH FRICTION REGIME : PROTON TRANSFER IN TRIOSEPHOSPHATE ISOMERASE (TIM)

Martin Karplus, M. Karplus, E. Neria, 1996 .

Effect of constraints on the dynamics of macromolecules

W. F. van Gunsteren, Martin Karplus, M. Karplus, 1982 .

Solution conformations of human growth hormone releasing factor: comparison of the restrained molecular dynamics and distance geometry methods for a system without long-range distance data.

M Karplus, A M Gronenborn, G M Clore, 1987, Protein engineering.

Phase diagram of a model protein derived by exhaustive enumeration of the conformations

Aaron R. Dinner, Andrej Sali, Eugene I. Shakhnovich, 1994 .

Multiple Conformations of RGDW and dRGDW: A Theoretical Study and Comparison with NMR Results

M. Karplus, R. Stote, A. Dejaegere, 2000 .

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method.

Martin Karplus, M. Karplus, A. van der Vaart, 2005, The Journal of chemical physics.

Analysis of two-residue turns in proteins.

M Karplus, G A Petsko, M. Karplus, 1994, Journal of molecular biology.

Quantitative Structure-Activity Relationship Studies of Progesterone Receptor Binding Steroids

Steven P. van Helden, Vincent J. van Geerestein, Sung-Sau So, 2000, J. Chem. Inf. Comput. Sci..

Cumulant expansion of the free energy: Application to free energy derivatives and component analysis

Martin Karplus, Georgios Archontis, M. Karplus, 1996 .

A Hybrid QM−MM Potential Employing Hartree−Fock or Density Functional Methods in the Quantum Region

Milan Hodošček, Martin Karplus, M. Karplus, 1999 .

Chaperoned alchemical free energy simulations: a general method for QM, MM, and QM/MM potentials.

Wei Yang, Martin Karplus, M. Karplus, 2004, The Journal of chemical physics.

Inertial effects in butane stochastic dynamics

M. Karplus, R. Pastor, 1989 .

Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly.

M. Karplus, A. Dinner, E. Verosub, 1999, Protein engineering.

Use of quantitative structure‐property relationships to predict the folding ability of model proteins

M. Karplus, S. So, A. Dinner, 1998, Proteins.

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process.

Amedeo Caflisch, Sergei V Krivov, Martin Karplus, 2008, The journal of physical chemistry. B.

Hydrodynamic description of protein folding.

Martin Karplus, M. Karplus, A. Palyanov, 2008, Physical review letters.

A lattice protein with an amyloidogenic latent state: stability and folding kinetics.

M. Karplus, A. Palyanov, S. Krivov, 2007, Journal of Physical Chemistry B.

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

Sergei V Krivov, Martin Karplus, M. Karplus, 2006, The journal of physical chemistry. B.

The roles of stability and contact order in determining protein folding rates

Aaron R. Dinner, Martin Karplus, M. Karplus, 2001, Nature Structural Biology.

Importance of metastable states in the free energy landscapes of polypeptide chains.

Michele Vendruscolo, Mark A Miller, Sergei V Krivov, 2007, Physical review letters.

An Integral Equation Theory Study of the Solvent-Induced Reaction Barrier in the Nucleophilic Addition of Hydroxide to Formaldehyde.

M. Karplus, Hsiang‐Ai Yu, 1990 .

The nature of the ion binding interactions in EF-hand peptide analogs: free energy simulation of Asp to Asn mutations.

M. Karplus, B. Prod'hom, 1993, Protein engineering.

Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 1. Method and validations.

M Karplus, M. Karplus, S. So, 1997, Journal of medicinal chemistry.

Generalized perturbed Hartree–Fock theory

M. Karplus, P. Rossky, 1980 .

Use of MCSS to design small targeted libraries: application to picornavirus ligands.

M Karplus, M. Karplus, D. Filman, 2001, Journal of the American Chemical Society.

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

Fabrice Leclerc, Christian Bartels, Michael Schaefer, 2001, J. Comput. Chem..

Quaternary structure and function in phage lambda repressor: 1H-NMR studies of genetically altered proteins.

M. Karplus, R. Sauer, M. Weiss, 1987, Journal of biomolecular structure & dynamics.

β‐Sheet coil transitions in a simple polypeptide model

M Karplus, D L Weaver, M. Karplus, 1992, Proteins.

Solution Conformation and Thermodynamics of Structured Peptides: Molecular Dynamics Simulation with

M. Karplus, C. Bartels, M. Schaefer, 1998 .

The folding mechanism of larger model proteins: role of native structure.

M Karplus, A Sali, M. Karplus, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling

Christian Bartels, Martin Karplus, M. Karplus, 1999 .

Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding

M. Karplus, C. Bartels, M. Schaefer, 1999 .

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

Christian Bartels, Martin Karplus, M. Karplus, 1997, J. Comput. Chem..

Karplus, Martin: Theory of Vicinal Coupling Constants

M. Karplus, 2007 .

FK506 and rapamycin binding to FKBP: common elements in immunophilin-ligand complexation

M. Karplus, S. Schreiber, S. Michnick, 1991 .

An Approach to the Internal Rotation Problem

M. Karplus, R. Parr, 1963 .

Note on the Internal‐Rotation Barrier in Ethanic Compounds

M. Karplus, 1960 .

Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition.

Michele Vendruscolo, Emanuele Paci, Martin Karplus, 2002, Biophysical journal.

Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements

Martin Karplus, Marco Cecchini, A. Houdusse, 2008, PLoS Comput. Biol..

Role of structural flexibility in conformational calculations. Application to acetylcholine and beta-methylacetylcholine.

M. Karplus, B. Gelin, 1975, Journal of the American Chemical Society.

ROLE OF STRUCTURAL FLEXIBILITY IN CONFORMATIONAL CALCULATIONS. APPLICATION TO ACETYLCHOLINE AND β-METHYLACETYLCHOLINE

M. Karplus, B. Gelin, 1976 .

Comment on the Communication “The Key to Solving the Protein‐Folding Problem Lies in an Accurate Description of the Denatured State” by van Gunsteren et al.

M. Karplus, A. Dinner, 2001 .

Analysis of Calculated Normal Modes of a Set of Native and Partially Unfolded Proteins

M. Karplus, H. Vlijmen, 1999 .

A comparison of the dynamic behavior of monomeric and dimeric insulin shows structural rearrangements in the active monomer.

Markus Meuwly, Vincent Zoete, Martin Karplus, 2004, Journal of molecular biology.

The allosteric mechanism of yeast chorismate mutase: a dynamic analysis.

M. Karplus, W. Lipscomb, Jianpeng Ma, 2006, Journal of molecular biology.

Factors that affect the folding ability of proteins

M Karplus, M. Karplus, E. Shakhnovich, 1998, Proteins.

A conformational transition in the myosin VI converter contributes to the variable step size.

M Karplus, M. Karplus, E. Vanden-Eijnden, 2011, Biophysical journal.

Statistical Analysis of Protein Folding Kinetics

M. Karplus, S. So, A. Dinner, 2002 .

STATISTICAL ANALYSIS OF PROTEIN FOLDING KINETICS

M. Karplus, S. So, A. U.S., 2002 .

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model.

M. Karplus, E. Lau, F. Lightstone, 2020, Journal of chemical theory and computation.

Many‐body perturbation theory applied to molecules: Analysis and correlation energy calculation for Li2, N2, and H3

M. Karplus, David L. Freemen, 1976 .

Chain closure with bond angle variations

Robert E. Bruccoleri, Martin Karplus, M. Karplus, 1985 .

Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation.

M Karplus, M. Karplus, S. Swaminathan, 1985, Biophysical journal.

Investigation of glucose binding sites on insulin

Markus Meuwly, Vincent Zoete, Martin Karplus, 2004, Proteins.

Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes.

Shunzhou Wan, Martin Karplus, Roland H Stote, 2004, The Journal of chemical physics.

The origin of protein sidechain order parameter distributions.

M. Karplus, J. Clarke, R. Best, 2004, Journal of the American Chemical Society.

A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes.

M. Karplus, K. Nam, V. Ovchinnikov, 2016, The journal of physical chemistry. B.

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

David Baker, Thomas Szyperski, Victor Ovchinnikov, 2018, Protein science : a publication of the Protein Society.

Comment on a "fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations".

M Karplus, M. Karplus, T. Ichiye, 1996, Journal of molecular biology.

An improved method for nonbonded list generation: Rapid determination of near‐neighbor pairs

Bernard R. Brooks, Ioan Andricioaei, Robert J. Petrella, 2003, J. Comput. Chem..

Generalized ensembles serve to improve the convergence of free energy simulations

Wei Yang, Martin Karplus, M. Karplus, 2003 .

Role of conformation transitions in adenylate kinase

Martin Karplus, M. Karplus, 2010, Proceedings of the National Academy of Sciences.

A charge-scaling method to treat solvent in QM/MM simulations

M. Karplus, A. Dinner, X. López, 2003 .

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

M. Karplus, K. Nam, G. Verdine, 2020, Nature Communications.

Free energy of sickling: A simulation analysis.

M Karplus, B Tidor, M. Karplus, 1990, Proceedings of the National Academy of Sciences of the United States of America.

Protein dynamics: From the native to the unfolded state and back again

Amedeo Caflisch, Eugene Shakhnovich, Martin Karplus, 1995 .

Solvent effects on the reaction coordinate of the hydrolysis of phosphates and sulfates: application of Hammond and anti-Hammond postulates to understand hydrolysis in solution.

M. Karplus, X. López, A. Dejaegere, 2001, Journal of the American Chemical Society.

A new two-disulphide intermediate in the refolding of reduced bovine pancreatic trypsin inhibitor.

M. Karplus, D. States, C. Dobson, 1984, Journal of molecular biology.

Quantum-Mechanical Calculation of One-Electron Properties. I. General Formulation

Leonard M. Isaacson, M. Karplus, A. Kuppermann, 1958 .

Conformational sampling via a self-regulating effective energy surface.

Wei Yang, Aaron R Dinner, Martin Karplus, 2006, The Journal of chemical physics.

Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water

M. Karplus, Hongyi Zhou, Yaoqi Zhou, 2006 .

Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis

Jeremy C. Smith, M. Karplus, B. Tidor, 1994 .

Role of Electrostatics in the Structure, Energy, and Dynamics of Biomolecules: A Model Study of N-Methylalanylacetamide

M. Karplus, B. Pettitt, 1985 .

Importance of attractive van der Waals contribution in empirical energy function models for the heat of vaporization of polar liquids

Alexander D. MacKerell, Martin Karplus, M. Karplus, 1991 .

Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin

M. Karplus, S. Schreiber, S. Michnick, 1991, Science.

Hydrogen Bond Energetics: A Simulation and Statistical Analysis of N-Methyl Acetamide (NMA), Water, and Human Lysozyme†

Matthias Buck, Martin Karplus, M. Karplus, 2001 .

Analysis of cooperativity in hemoglobin. Valency hybrids, oxidation, and methemoglobin replacement reactions.

M. Karplus, A. Szabó, 1975, Biochemistry.

MCSS functionality maps for a flexible protein

Collin M. Stultz, M Karplus, M. Karplus, 1999, Proteins.

Schrödinger: Molecular dynamics: from H+H2 to biomolecules

M. Karplus, 1987 .

Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 2. Applications.

M Karplus, M. Karplus, S. So, 1997, Journal of medicinal chemistry.

Theoretical Investigations of Reactive Collisions in Molecular Beams: K +CH3I

M. Karplus, L. Raff, 1964 .

Unsuspected pathway of the allosteric transition in hemoglobin

M. Karplus, Stefan Fischer, K. Nam, 2011, Proceedings of the National Academy of Sciences.

DYNAMICS OF ORGANIC REACTIONS

Martin Karplus, M. Karplus, I. S. Y. Wang, 1974 .

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

M. Karplus, G. Crooks, F. Ritort, 2007, The Journal of chemical physics.

Analysis of Coupling Schemes in Free Energy Simulations: A Unified Description of Nonbonded Contributions to Solvation Free Energies

M. Karplus, A. Dejaegere, M. Karplus, 1996 .

Simulation analysis of structures on the reaction pathway of RNAse A

M. Karplus, C. Lim, A. Brunger, 1990 .

Exploration of partially unfolded states of human α-lactalbumin by molecular dynamics simulation

Christopher M. Dobson, Emanuele Paci, Martin Karplus, 2001 .

Amino-terminal arm of the repressor: a proton NMR study

M. Karplus, R. Sauer, D. Patel, 1984 .

A comparison of the restrained molecular dynamics and distance geometry methods for determining three‐dimensional structures of proteins on the basis of interproton distances

M. Karplus, A. Gronenborn, G. Clore, 1987, FEBS letters.

Discrimination of the native from misfolded protein models with an energy function including implicit solvation.

M. Karplus, T. Lazaridis, 1999, Journal of molecular biology.

Spatially constrained minimization of macromolecules

M. Karplus, R. Bruccoleri, 1986, Journal of Computational Chemistry.

Distortional Effects on the Ethane Internal‐Rotation Barrier

M. Karplus, O. Sovers, 1966 .

On the Determination of the Phases of Electromagnetic Scattering Amplitudes from Experimental Data

M. Karplus, R. Gerber, 1972 .

``Average Energy Approximation'' in Spin‐Coupling Calculations

M. Karplus, 1960 .

Harmonic analysis of large systems. II. Comparison of different protein models

Dusanka Janezic, Martin Karplus, M. Karplus, 1995, J. Comput. Chem..

Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation

Robert J. Petrella, Martin Karplus, M. Karplus, 2005, J. Comput. Chem..

SOLVATION OF A DIPEPTIDE BY WATER *

M. Karplus, P. Rossky, 1981 .

NMR characterization of DNA: assignment of major groove sugar protons of the .lambda.-phage operator site OL1 by two-dimensional NOE and J-correlated spectra

M. Karplus, R. Sauer, D. Patel, 1984 .

Many‐body perturbation theory applied to molecules: Analysis and correlation energy calculation for Li2, N2, and H3

M. Karplus, David L. Freemen, 1976 .

Asymptotic Expansion Method for Franck–Condon Factors of Morse Oscillators

Martin Karplus, M. Karplus, T. Chang, 1970 .

Characterization of flexible molecules in solution: the RGDW peptide.

M Karplus, M. Karplus, C. Bartels, 1998, Journal of molecular biology.

Ligand binding and protein relaxation in heme proteins: a room temperature analysis of NO geminate recombination.

M Karplus, M. Karplus, K. Kuczera, 1991, Biochemistry.

Mechanical coupling in myosin V: a simulation study.

M. Karplus, B. Trout, V. Ovchinnikov, 2009, Journal of molecular biology.

A POISSON-BOLTZMANN STUDY OF CHARGE INSERTION IN AN ENZYME ACTIVE SITE : THE EFFECT OF DIELECTRIC RELAXATION

Thomas Simonson, Martin Karplus, Georgios Archontis, 1999 .

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior.

M Karplus, M. Karplus, R. Levy, 1982, Proceedings of the National Academy of Sciences of the United States of America.

The structure of water surrounding a peptide: a theoretical approach

M. Karplus, B. Pettitt, 1987 .

Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding.

Thomas Simonson, Martin Karplus, Georgios Archontis, 1997 .

Structure of proteins with single-site mutations: a minimum perturbation approach.

M Karplus, M. Karplus, J. Brady, 1985, Proceedings of the National Academy of Sciences of the United States of America.

Mechanism of Alkaline Hydrolysis of Cyclic and Acyclic Sulfates: An ab Initio Study with Solvation Correction

M. Karplus, X. López, A. Dejaegere, 1999 .

Corrigendum: Behind the folding funnel diagram

M. Karplus, 2011 .

Folding time distributions as an approach to protein folding kinetics.

M. Karplus, S. Krivov, S. Chekmarev, 2005, The journal of physical chemistry. B.

Diffusion-Collision Model for the Folding Kinetics of the λ-Repressor Operator-Binding Domain

Donald Bashford, David L. Weaver, Martin Karplus, 1984 .

On the Treatment of Electrostatic Interactions in Biomolecular Simulations

M. Karplus, D. States, R. Stote, 1991 .

Potential energy surface and molecular dynamics of MbNO: existence of an unsuspected FeON minimum.

M. Karplus, M. Meuwly, D. R. Nutt, 2005, The journal of physical chemistry. B.

Configuration entropy of the alanine dipeptide in vacuum and in solution: a molecular dynamics study

Martin Karplus, John W. Brady, M. Karplus, 1985 .