Martin Karplus

26 papers Journal 25Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	High-throughput molecular simulations of SARS-CoV-2 receptor binding domain mutants quantify correlations between dynamic fluctuations and protein expression. J. Comput. Chem. Victor Ovchinnikov, Martin Karplus
2022	J	`jnl`	Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV. PLoS Comput. Biol. Simone Conti, Victor Ovchinnikov, Jonathan G. Faris, Arup K. Chakraborty, Martin Karplus, Kayla G. Sprenger
2022	J	`jnl`	ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning. J. Comput. Chem. Simone Conti, Victor Ovchinnikov, Martin Karplus
2019	J	`jnl`	Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning. PLoS Comput. Biol. Simone Conti, Martin Karplus
2009	J	`jnl`	CHARMM: The biomolecular simulation program. J. Comput. Chem. Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
2008	J	`jnl`	Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements. PLoS Comput. Biol. Marco Cecchini, Anne Houdusse, Martin Karplus
2007	J	`jnl`	Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. J. Comput. Aided Mol. Des. Erik Evensen, Diane Joseph-McCarthy, Gregory A. Weiss, Stuart L. Schreiber, Martin Karplus
2005	J	`jnl`	Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation. J. Comput. Chem. Robert J. Petrella, Martin Karplus
2003	J	`jnl`	An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. J. Comput. Chem. Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus
2003	J	`jnl`	Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis. J. Comput. Chem. Marcus Elstner, Qiang Cui, Petra Munih, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus
2003	J	`jnl`	Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. J. Comput. Aided Mol. Des. Vincent Zoete, Olivier Michielin, Martin Karplus
2001	J	`jnl`	Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. J. Comput. Chem. Michael Schaefer, Christian Bartels, Fabrice Leclerc, Martin Karplus
2001	J	`jnl`	Evaluation of designed ligands by a multiple screening method: Application to glycogen phosphorylase inhibitors constructed with a variety of approaches. J. Comput. Aided Mol. Des. Sung-Sau So, Martin Karplus
2001	J	`jnl`	Functional group placement in protein binding sites: a comparison of GRID and MCSS. J. Comput. Aided Mol. Des. Ryan Bitetti-Putzer, Diane Joseph-McCarthy, James M. Hogle, Martin Karplus
2000	J	`jnl`	Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. J. Comput. Aided Mol. Des. Amedeo Caflisch, Hans J. Schramm, Martin Karplus
2000	J	`jnl`	Quantitative Structure-Activity Relationship Studies of Progesterone Receptor Binding Steroids. J. Chem. Inf. Comput. Sci. Sung-Sau So, Steven P. van Helden, Vincent J. van Geerestein, Martin Karplus
1999	J	`jnl`	A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J. Comput. Aided Mol. Des. Sung-Sau So, Martin Karplus
1997	J	`jnl`	Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. J. Comput. Chem. Amedeo Caflisch, Stefan Fischer, Martin Karplus
1997	J	`jnl`	Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations. J. Comput. Chem. Christian Bartels, Martin Karplus
1996	J	`jnl`	Functionality map analysis of the active site cleft of human thrombin. J. Comput. Aided Mol. Des. Peter D. J. Grootenhuis, Martin Karplus
1996	J	`jnl`	New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities. J. Comput. Chem. Arnaud Blondel, Martin Karplus
1995	J	`jnl`	Harmonic Analysis of Large Systems. I. Methodology. J. Comput. Chem. Bernard R. Brooks, Dusanka Janezic, Martin Karplus
1995	J	`jnl`	Harmonic Analysis of Large Systems. II. Comaprison of Different Protein Models. J. Comput. Chem. Dusanka Janezic, Martin Karplus
1995	J	`jnl`	Harmonic Analysis of Large Systems. III. Comparison with Molecular Dynamics. J. Comput. Chem. Dusanka Janezic, Richard M. Venable, Martin Karplus
1995	J	`jnl`	Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. J. Comput. Chem. Benoît Roux, Martin Karplus
1995	—	`conf`	Thermodynamics and kinetics of protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding Andrej Sali, Eugene I. Shakhnovich, Martin Karplus