The emergence of protein dynamics simulations: how computational statistical mechanics met biochemistry

[1]  Daniele Macuglia.  Giovanni Battimelli; Giovanni Ciccotti; Pietro Greco. Computer Meets Theoretical Physics: The New Frontier of Molecular Simulation. Translated by G. Giobbi. (The Frontiers Collection.) 206 pp., bibl., index. Berlin: Springer, 2020. €39.51 (cloth); ISBN 9783030393984. Paper and e-book available. , 2022, Isis.

[2]  M. Parrinello,et al.  Deep learning the slow modes for rare events sampling , 2021, Proceedings of the National Academy of Sciences.

[3]  G. Ciccotti,et al.  The breakthrough of a quantum chemist by classical dynamics: Martin Karplus and the birth of computer simulations of chemical reactions , 2021, The European Physical Journal H.

[4]  G. Ciccotti,et al.  The breakthrough of a quantum chemist by classical dynamics: Martin Karplus and the birth of computer simulations of chemical reactions , 2021, The European Physical Journal H.

[5]  T. Haigh,et al.  A New History of Modern Computing , 2021 .

[6]  M. Karplus.  Spinach on the Ceiling , 2020 .

[7]  Andrew L. Ferguson,et al.  Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation , 2020, Molecular Physics.

[8]  Giovanni Ciccotti,et al.  Sense Experiences and “Necessary Simulations”: Four Centuries of Scientific Change from Galileo to Fundamental Computer Simulations , 2020, KNOW: A Journal on the Formation of Knowledge.

[9]  Giovanni Ciccotti,et al.  Computer Meets Theoretical Physics , 2020 .

[10]  M. Mareschal.  From Varenna (1970) to Como (1995): Kurt Binder’s long walk in the land of criticality , 2019, The European Physical Journal H.

[11]  G. Ciccotti,et al.  Berni Alder and the pioneering times of molecular simulation , 2018, The European Physical Journal H.

[12]  Ushnish Sengupta,et al.  Markov models for the elucidation of allosteric regulation , 2018, Philosophical Transactions of the Royal Society B: Biological Sciences.

[13]  M. Mareschal.  Early years of Computational Statistical Mechanics , 2018 .

[14]  J Andrew McCammon,et al.  Autobiography of J. Andrew McCammon. , 2016, The journal of physical chemistry. B.

[15]  Martin Karplus,et al.  Development of Multiscale Models for Complex Chemical Systems: From H + H2 to Biomolecules (Nobel Lecture) , 2014 .

[16]  M. Karplus.  Development of multiscale models for complex chemical systems: from H+H₂ to biomolecules (Nobel Lecture). , 2014, Angewandte Chemie.

[17]  Arieh Warshel,et al.  Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). , 2014, Angewandte Chemie.

[18]  Johanna L. Miller.  Chemistry Nobel honors computer simulation of biomolecules , 2013 .

[19]  J. Changeux.  The origins of allostery: from personal memories to material for the future. , 2013, Journal of molecular biology.

[20]  Alan E Mark,et al.  Wilfred van Gunsteren: 35 Years of Biomolecular Simulation. , 2012, Journal of chemical theory and computation.

[21]  Tamar Schlick,et al.  Molecular Modeling and Simulation: An Interdisciplinary Guide , 2010 .

[22]  J. P. Grossman,et al.  Millisecond-scale molecular dynamics simulations on Anton , 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

[23]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[24]  N. Jaidane,et al.  Potential energy surface for the , 2008 .

[25]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[26]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[27]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[28]  B. Roux,et al.  Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands , 2004, Nature.

[29]  K. Schulten,et al.  Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning , 2002, Science.

[30]  B. Roux,et al.  Energetics of ion conduction through the K + channel , 2022 .

[31]  M. Levitt.  The birth of computational structural biology , 2001, Nature Structural Biology.

[32]  Giulio Superti-Furga,et al.  Dynamic Coupling between the SH2 and SH3 Domains of c-Src and Hck Underlies Their Inactivation by C-Terminal Tyrosine Phosphorylation , 2001, Cell.

[33]  G. Schatz.  Perspective on “Exchange reactions with activation energy. I. Simple barrier potential for (H, H2)” , 2000 .

[34]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[35]  M. Mehedintu.  Biological membranes. A molecular perspective from computation and experiment , 1997 .

[36]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197 , 1996 .

[37]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[38]  Emerson W. Pugh,et al.  IBM's 360 and early 370 systems , 1991 .

[39]  M. Karplus,et al.  Molecular dynamics simulations in biology , 1990, Nature.

[40]  M. Karplus,et al.  Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. , 1989, Science.

[41]  C. Brooks.  Computer simulation of liquids , 1989 .

[42]  R. Sharon,et al.  Accurate simulation of protein dynamics in solution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[43]  M. Karplus.  Molecular Dynamics Simulations of Proteins , 1987 .

[44]  P. A. Bash,et al.  Free energy calculations by computer simulation. , 1987, Science.

[45]  P. A. Bash,et al.  Calculation of the relative change in binding free energy of a protein-inhibitor complex. , 1987, Science.

[46]  D. Frenkel,et al.  Simulation of liquids and solids : molecular dynamics and Monte Carlo methods in statistical mechanics , 1987 .

[47]  H. L. Anderson.  Scientific uses of the MANIAC , 1986 .

[48]  J A McCammon,et al.  Theoretical calculation of relative binding affinity in host-guest systems. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[49]  M. Karplus,et al.  Electronic structure of the MoFe3S4(SH)3−6 ion: A broken‐symmetry metal–sulfur cluster , 1985 .

[50]  W. L. Jorgensen,et al.  Monte Carlo simulation of differences in free energies of hydration , 1985 .

[51]  K Nagayama,et al.  [Dynamics proteins]. , 1985, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[52]  M. Ehrenberg,et al.  Biomolecular dynamics: A report from a workshop in Gysinge, Sweden, October 4–7, 1982 , 1984, Quarterly Reviews of Biophysics.

[53]  James Andrew McCammon,et al.  Ligand-receptor interactions , 1984, Comput. Chem..

[54]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[55]  R. Levy,et al.  Protein dynamics and NMR relaxation: comparison of simulations with experiment , 1982, Nature.

[56]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results , 1982 .

[57]  M Karplus,et al.  Dynamical theory of activated processes in globular proteins. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[58]  H. Berendsen,et al.  THERMODYNAMICS OF CAVITY FORMATION IN WATER - A MOLECULAR-DYNAMICS STUDY , 1982 .

[59]  R. Baxter.  Exactly solved models in statistical mechanics , 1982 .

[60]  A. Szabó,et al.  Effect of librational motion on fluorescence depolarization and nuclear magnetic resonance relaxation in macromolecules and membranes. , 1980, Biophysical journal.

[61]  M. Karplus,et al.  Dynamics of activated processes in globular proteins. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Martin Karplus,et al.  SOLVATION. A MOLECULAR DYNAMICS STUDY OF A DIPEPTIDE IN WATER. , 1979 .

[63]  M. Karplus,et al.  A model for the simulation of an aqueous dipeptide solution , 1979 .

[64]  A. Szabó,et al.  Theory of NMR relaxation in macromolecules: Restricted diffusion and jump models for multiple internal rotations in amino acid side chains , 1978 .

[65]  David Chandler,et al.  Statistical mechanics of isomerization dynamics in liquids and the transition state approximation , 1978 .

[66]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[67]  Charles H. Bennett,et al.  Molecular Dynamics and Transition State Theory: The Simulation of Infrequent Events , 1977 .

[68]  M Karplus,et al.  Mechanism of tertiary structural change in hemoglobin. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[69]  P. Wolynes,et al.  Nonsteady hydrodynamics of biopolymer motions , 1977 .

[70]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[71]  Charles H. Bennett,et al.  Efficient estimation of free energy differences from Monte Carlo data , 1976 .

[72]  M. Karplus,et al.  The hinge-bending mode in lysozyme , 1976, Nature.

[73]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[74]  Arieh Warshel,et al.  Bicycle-pedal model for the first step in the vision process , 1976, Nature.

[75]  D. W. Noid.  Studies in Molecular Dynamics , 1976 .

[76]  M. Karplus,et al.  Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[77]  D. Ermak.  A computer simulation of charged particles in solution. I. Technique and equilibrium properties , 1975 .

[78]  M. Karplus,et al.  Semiclassical trajectory approach to photoisomerization , 1975 .

[79]  M. Karplus,et al.  Theoretical studies of the visual chromophore , 1975 .

[80]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[81]  J. Deisenhofer,et al.  Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution , 1975 .

[82]  F. Stillinger,et al.  Improved simulation of liquid water by molecular dynamics , 1974 .

[83]  B. Honig,et al.  The structure and spectra of the chromophore of the visual pigments. , 1974, Annual review of biophysics and bioengineering.

[84]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[85]  M. Karplus,et al.  Interpretation of the binding of carbon monoxide to hemoglobin under photodissociating conditions. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[86]  M Karplus,et al.  A mathematical model for structure-function relations in hemoglobin. , 1972, Journal of molecular biology.

[87]  Martin Karplus,et al.  Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization , 1972 .

[88]  M. Karplus,et al.  A mathematical model for structure-function relationships in hemoglobin. , 1972, Biochemical and biophysical research communications.

[89]  F. Stillinger,et al.  Molecular Dynamics Study of Liquid Water , 1971 .

[90]  M. Perutz,et al.  Molecular Pathology of Human Haemoglobin: Stereochemical Interpretation of Abnormal Oxygen Affinities , 1971, Nature.

[91]  J. Karle,et al.  Crystal Structure of the Visual Chromophores, 11-cis and all-trans Retinal , 1971, Nature.

[92]  M. Karplus,et al.  Collision Dynamics and the Statistical Theories of Chemical Reactions. II. Comparison of Reaction Probabilities , 1971 .

[93]  M. Karplus,et al.  Ring orientation in -ionone and retinals. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[94]  M. Perutz,et al.  Three dimensional structure of haemoglobin Rainier. , 1971, Nature: New biology.

[95]  M. Karplus,et al.  Electronic structure of cyanide complexes of hemes and heme proteins. , 1971, Journal of molecular biology.

[96]  M. Karplus,et al.  Implications of Torsional Potential of Retinal Isomers for Visual Excitation , 1971, Nature.

[97]  M. Perutz.  Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery , 1970, Nature.

[98]  M. Karplus,et al.  Atoms and Molecules: An Introduction for Students of Physical Chemistry , 1970 .

[99]  The Bohr Effect and Combination with Organic Phosphates , 1970, Nature.

[100]  M. Karplus,et al.  Collision Dynamics and the Statistical Theories of Chemical Reactions. I. Average Cross Section from Transition‐State Theory , 1969 .

[101]  M. Levitt,et al.  Refinement of protein conformations using a macromolecular energy minimization procedure. , 1969, Journal of molecular biology.

[102]  M. Karplus,et al.  Spin Delocalization and Vibrational–Electronic Interaction in the Toluene Ion–Radicals , 1969 .

[103]  M. Karplus,et al.  Perturbed Hartree–Fock Theory. I. Diagrammatic Double‐Perturbation Analysis , 1969 .

[104]  A. Warshel,et al.  Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules , 1968 .

[105]  L. Pauling,et al.  Structural chemistry and molecular biology , 1968 .

[106]  M. Karplus,et al.  Deuterium Isotope Effects in the Electron Spin Resonance Spectra of Naphthalene Negative Ions , 1967 .

[107]  Clarence B. Germain.  Programming the IBM 360 , 1967 .

[108]  M. Karplus,et al.  Quasiclassical Trajectory Analysis for the Reaction of Potassium Atoms with Oriented Methyl Iodide Molecules1 , 1966 .

[109]  Martin Karplus,et al.  Exchange Reactions with Activation Energy. I. Simple Barrier Potential for (H, H2) , 1965 .

[110]  J. Changeux,et al.  ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.

[111]  J. Changeux.  ALLOSTERIC INTERACTIONS INTERPRETED IN TERMS OF QUATERNARY STRUCTURE. , 1964, Brookhaven symposia in biology.

[112]  Aneesur Rahman,et al.  Correlations in the Motion of Atoms in Liquid Argon , 1964 .

[113]  Martin Karplus,et al.  Dynamics of Reactive Collisions: The H +H2 Exchange Reaction , 1964 .

[114]  M. Karplus,et al.  Potential Energy Surface for H3 , 1964 .

[115]  M. Karplus,et al.  Potential-Energy Surface for H 3 , 1964 .

[116]  Martin Karplus,et al.  Vicinal Proton Coupling in Nuclear Magnetic Resonance , 1963 .

[117]  J. Changeux,et al.  The feedback control mechanisms of biosynthetic L-threonine deaminase by L-isoleucine. , 1961, Cold Spring Harbor symposia on quantitative biology.

[118]  B. Alder,et al.  Studies in Molecular Dynamics. I. General Method , 1959 .

[119]  M. Karplus.  Contact Electron‐Spin Coupling of Nuclear Magnetic Moments , 1959 .

[120]  B. Alder,et al.  Phase Transition for a Hard Sphere System , 1957 .

[121]  R. Zwanzig.  High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[122]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[123]  J. Kirkwood.  Statistical Mechanics of Fluid Mixtures , 1935 .

[124]  M. Karplus,et al.  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 ) , 2022 .