Kenneth M. Merz

发表

MCPB.py: A Python Based Metal Center Parameter Builder

Pengfei Li, Kenneth M. Merz, K. Merz, 2016, J. Chem. Inf. Model..

Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems

Dimas Suárez, Kenneth M. Merz, Arjan van der Vaart, 2000 .

Molecular dynamics simulations of the dinuclear zinc‐β‐lactamase from Bacteroides fragilis complexed with imipenem

Dimas Suárez, Natalia Díaz, Kenneth M. Merz, 2002, J. Comput. Chem..

The application of the genetic algorithm to the minimization of potential energy functions

Kenneth M. Merz, Scott M. Le Grand, K. Merz, 1993, J. Glob. Optim..

Comment on “a minimal implementation of the AMBER–GAUSSIAN interface for Ab Initio QM/MM‐MD simulation”

Adrian E. Roitberg, Kenneth M. Merz, Erik Deumens, 2012, J. Comput. Chem..

Introducing the Review Manuscript Type

Kenneth M. Merz, 2015, J. Chem. Inf. Model..

Drug Design: Drug Design

Kenneth M. Merz, Dagmar Ringe, Charles H. Reynolds, 2010 .

Nuclear magnetic resonance simulations

Kenneth M. Merz, Alan J. Benesi, James J. Vincent, 1999 .

JCIM Special Issue on Generative Models for Molecular Design

Gianni De Fabritiis, Kenneth M. Merz, Guowei Wei, 2020, Journal of Chemical Information and Modeling.

On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

Zheng Zheng, Kenneth M. Merz, Nupur Bansal, 2016, Journal of Computer-Aided Molecular Design.

Ligand Identification Scoring Algorithm (LISA)

Zheng Zheng, Kenneth M. Merz, K. Merz, 2011, J. Chem. Inf. Model..

OSiRIS: A Distributed Storage and Networking Project Update

Ezra Kissel, Kenneth M. Merz, Shawn McKee, 2020, EPJ Web of Conferences.

The Amber biomolecular simulation programs

Holger Gohlke, Ray Luo, Bing Wang, 2005, J. Comput. Chem..

Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores

Zheng Zheng, Kenneth M. Merz, John C. Faver, 2012, Journal of Computer-Aided Molecular Design.

Drug Design: STRUCTURAL BIOLOGY

Kenneth M. Merz, Charles H. Reynolds, Dagmar Ringe, 2010 .

New Manuscript Type: Application Note

Kenneth M. Merz, 2014, J. Chem. Inf. Model..

Update to Our Reader, Reviewer, and Author Communities - April 2020

Sébastien Lecommandoux, Harry A. Atwater, Kenneth M. Merz, 2020, Journal of Chemical Information and Modeling.

Letter from the Editors

Matthias Rarey, Alexander Tropsha, Kenneth M. Merz, 2015, J. Chem. Inf. Model..

Reduction of Urease Activity by Interaction with the Flap Covering the Active Site

Kenneth M. Merz, Robert P. Hausinger, Lee Macomber, 2015, J. Chem. Inf. Model..

Accurate assessment of the strain energy in a protein‐bound drug using QM/MM X‐ray refinement and converged quantum chemistry

Xue Li, Zheng Fu, Kenneth M. Merz, 2011, J. Comput. Chem..

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions

Zheng Zheng, Kenneth M. Merz, K. Merz, 2013, J. Chem. Inf. Model..

A force field for monosaccharides and (1 → 4) linked polysaccharides

Kenneth M. Merz, Scott M. Le Grand, Timothy M. Glennon, 1994, J. Comput. Chem..

A highly portable parallel implementation of AMBER4 using the message passing interface standard

Kenneth M. Merz, James J. Vincent, 1995, J. Comput. Chem..

Computation of the physio‐chemical properties and data mining of large molecular collections

Kenneth M. Merz, Steven L. Dixon, Ailan Cheng, 2002, J. Comput. Chem..

Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tables

Kenneth M. Merz, Scott M. Le Grand, K. Merz, 1993, J. Comput. Chem..

Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method

Kenneth M. Merz, Steven L. Dixon, Arjan van der Vaart, 2000, J. Comput. Chem..

QMQSAR: Utilization of a semiempirical probe potential in a field‐based QSAR method

Kenneth M. Merz, Steven L. Dixon, S. L. Dixon, 2005, J. Comput. Chem..

An examination of a density functional/molecular mechanical coupled potential

Kenneth M. Merz, Robert V. Stanton, David S. Hartsough, 1995, J. Comput. Chem..

Quantum mechanical and molecular dynamics simulations of ureases and Zn β‐lactamases

Dimas Suárez, Kenneth M. Merz, Guillermina Estiu, 2006, Journal of computational chemistry.

Drug Design: Preface

Kenneth M. Merz, Charles H. Reynolds, Dagmar Ringe, 2010 .

Detailed potential of mean force studies on host–guest systems from the SAMPL6 challenge

Zheng Zheng, Kenneth M. Merz, Lin Frank Song, 2018, Journal of Computer-Aided Molecular Design.

Acceleration of High Angular Momentum Electron Repulsion Integrals and Integral Derivatives on Graphics Processing Units.

Kenneth M. Merz, Yipu Miao, K. Merz, 2015, Journal of chemical theory and computation.

QM/MM refinement and analysis of protein bound retinoic acid

Xue Li, Zheng Fu, Kenneth M. Merz, 2012, J. Comput. Chem..

The Ecstasy and Agony of Assay Interference Compounds.

Shaomeng Wang, Kenneth M. Merz, Carolyn Bertozzi, 2017, Journal of chemical information and modeling.

Can we separate active from inactive conformations?

Kenneth M. Merz, David J. Diller, K. Merz, 2002, J. Comput. Aided Mol. Des..

Performance of Density Functionals with Small Split Valence Basis Sets

Kenneth M. Merz, 2004 .

Are Many-Body Effects Important in Protein Folding?

Charles L. Brooks, Kenneth M. Merz, Arjan van der Vaart, 2000 .

Computer simulation of enzymatic reactions

Kenneth M. Merz, 1993 .

Dynamic Force Field Models: Molecular Dynamics Simulations of Human Carbonic Anhydrase II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential

Kenneth M. Merz, David S. Hartsough, D. Hartsough, 1995 .

Free energy perturbation simulations of the inhibition of thermolysin: prediction of the free energy of binding of a new inhibitor

Peter A. Kollman, Kenneth M. Merz, P. Kollman, 1989 .

Gas-phase and solution-phase potential energy surfaces for CO2 + nH2O (n = 1,2)

Kenneth M. Merz, K. Merz, 1990 .

Rationalization of the enantioselectivity of subtilisin in DMF

Kenneth M. Merz, Giorgio Colombo, Samuel Toba, 1999 .

Mechanism of the human carbonic anhydrase II-catalyzed hydration of carbon dioxide

Kenneth M. Merz, K. Merz, Ya-Jun Zheng, 1992 .

Fully Quantum Mechanical Description of Proteins in Solution. Combining Linear Scaling Quantum Mechanical Methodologies with the Poisson−Boltzmann Equation

Kenneth M. Merz, Valentin Gogonea, K. Merz, 1999 .

The Energy Computation Paradox and ab initio Protein Folding

Kenneth M. Merz, Bing Wang, John C. Faver, 2011, PloS one.

A carbohydrate force field for amber and its application to the study of saccharide to surface adsorption

Kenneth M. Merz, Timothy M. Glennon, K. Merz, 1997 .

Free energy calculations on the relative solvation free energies of benzene, anisole and 1,2,3-trimethoxybenzene : theoretical and experimental analysis of aromatic methoxy solvation

Peter A. Kollman, Kenneth M. Merz, Robert N. Hunter, 1991 .

Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian

Kenneth M. Merz, Lance M. Westerhoff, Valentin Gogonea, 2000 .

Acylation of Class A β-lactamases by Penicillins: A Theoretical Examination of the Role of Serine 130 and the β-lactam Carboxylate Group

Dimas Suárez, Natalia Díaz, Kenneth M. Merz, 2001 .

Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”

Kenneth M. Merz, John C. Faver, Melek N. Ucisik, 2014, Journal of chemical theory and computation.

Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems

Kenneth M. Merz, K. Merz, G. Monard, 1999 .

Divide and Conquer Interaction Energy Decomposition

Kenneth M. Merz, K. Merz, A. V. D. Vaart, 1999 .

Binding of Bicarbonate to Human Carbonic Anhydrase II: A Continuum of Binding States

Kenneth M. Merz, Lucia Banci, K. Merz, 1997 .

Density functional transition states of organic and organometallic reactions

Kenneth M. Merz, Robert V. Stanton, K. Merz, 1994 .

An Examination of a Hartree-Fock/Molecular Mechanical Coupled Potential

Kenneth M. Merz, Robert V. Stanton, K. Merz, 1995 .

Simulations of allosteric motions in the zinc sensor CzrA.

Bing Wang, Kenneth M. Merz, Dhruva K. Chakravorty, 2012, Journal of the American Chemical Society.

Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials

Kenneth M. Merz, Robert V. Stanton, 2002 .

Sodium parameters for AM1 and PM3 optimized using a modified genetic algorithm

Kenneth M. Merz, K. Merz, 2002 .

Stability and Activity of Mesophilic Subtilisin E and Its Thermophilic Homolog: Insights from Molecular Dynamics Simulations

Kenneth M. Merz, Giorgio Colombo, K. Merz, 1999 .

Application of the Nosé−Hoover Chain Algorithm to the Study of Protein Dynamics

Kenneth M. Merz, Ailan Cheng, K. Merz, 1996 .

Mode of action of carbonic anhydrase

Kenneth M. Merz, Roald Hoffmann, Michael J. S. Dewar, 1989 .

The Role of Polarization and Charge Transfer in the Solvation of Biomolecules

Kenneth M. Merz, K. Merz, Arjan van der Vaart and, 1999 .

Charge Transfer in Biologically Important Molecules: Comparison of High-Level ab initio and Semiempirical Methods

Kenneth M. Merz, Arjan van der Vaart, K. Merz, 2000 .

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Kenneth M. Merz, K. Merz, Ya-Jun Zheng, 1992 .

Importance of dispersion and electron correlation in ab initio protein folding.

Kenneth M. Merz, Guanglei Cui, Xiao He, 2009, The journal of physical chemistry. B.

CO2 binding to human carbonic anhydrase II

Kenneth M. Merz, K. Merz, 1991 .

Drug Design : Structure-and Ligand-Based Approaches

Kenneth M. Merz, Charles H. Reynolds, Dagmar Ringe, 2017 .

The Protein Folding Problem and Tertiary Structure Prediction

Kenneth M. Merz, Scott M. Le Grand, K. Merz, 2012 .

Zinc Metallo-β-Lactamase from Bacteroides fragilis: A Quantum Chemical Study on Model Systems of the Active Site

Dimas Suárez, Natalia Díaz, Kenneth M. Merz, 2000 .

3,4-connected carbon nets: through-space and through-bond interactions in the solid state

Kenneth M. Merz, Alexandru T. Balaban, Roald Hoffmann, 1987 .

Chapter 9 Calculating Binding Free Energy in Protein–Ligand Interaction

Kenneth M. Merz, Kaushik Raha, K. Merz, 2005 .

Calculation of solvation free energies using a density functional/molecular dynamics coupled potential

Kenneth M. Merz, Robert V. Stanton, David S. Hartsough, 1993 .

Theoretical investigation of the CO2 + OH- → HCO3- reaction in the gas and aqueous phases

Kenneth M. Merz, K. Merz, Z. Peng, 1993 .

Force Field Design for Metalloproteins

Kenneth M. Merz, K. Merz, Stephen C. Hoops, 1991 .

Determination of pKas of ionizable groups in proteins: The pKa of Glu 7 and 35 in hen egg white lysozyme and Glu 106 in human carbonic anhydrase II

Kenneth M. Merz, K. Merz, 1991 .

Free energy calculations on protein stability: Thr-157 .fwdarw. Val-157 mutation of T4 lysozyme

Peter A. Kollman, Kenneth M. Merz, P. Kollman, 1989 .

Inhibition of carbonic anhydrase

Mark A. Murcko, Peter A. Kollman, Kenneth M. Merz, 1991 .

Amber 2015, University of California, San Francisco

Holger Gohlke, Ray Luo, Adrian E. Roitberg, 2015 .

Free Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison with Continuum GB/SA Calculations

Kenneth M. Merz, Charles H. Reynolds, K. Merz, 1999 .

Computer modeling of the interactions of complex molecules

Peter A. Kollman, Kenneth M. Merz, P. Kollman, 1990 .

Solvent Dynamics and Mechanism of Proton Transfer in Human Carbonic Anhydrase II

Kenneth M. Merz, Giorgio Colombo, Samuel Toba, 1999 .