Martin Karplus

According to our database, Martin Karplus authored at least 25 papers between 1995 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.

Simone Conti, Victor Ovchinnikov, Jonathan G. Faris, Arup K. Chakraborty, Martin Karplus, Kayla G. Sprenger

PLoS Comput. Biol., 2022

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

Simone Conti, Victor Ovchinnikov, Martin Karplus

J. Comput. Chem., 2022

2019

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

Simone Conti, Martin Karplus

PLoS Comput. Biol., 2019

2009

CHARMM: The biomolecular simulation program.

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

J. Comput. Chem., 2009

2008

Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements.

Marco Cecchini, A. Houdusse, Martin Karplus

PLoS Comput. Biol., 2008

2007

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

Erik Evensen, Diane Joseph-McCarthy, Gregory A. Weiss, Stuart L. Schreiber, Martin Karplus

J. Comput. Aided Mol. Des., 2007

2005

Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation.

Robert J. Petrella, Martin Karplus

J. Comput. Chem., 2005

2003

An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs.

Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus

J. Comput. Chem., 2003

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

Marcus Elstner, Qiang Cui, Petra Munih, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus

J. Comput. Chem., 2003

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

Vincent Zoete, Olivier Michielin, Martin Karplus

J. Comput. Aided Mol. Des., 2003

2001

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes.

Michael Schaefer, Christian Bartels, Fabrice Leclerc, Martin Karplus

J. Comput. Chem., 2001

Evaluation of designed ligands by a multiple screening method: Application to glycogen phosphorylase inhibitors constructed with a variety of approaches.

Sung-Sau So, Martin Karplus

J. Comput. Aided Mol. Des., 2001

Functional group placement in protein binding sites: a comparison of GRID and MCSS.

Ryan Bitetti-Putzer, Diane Joseph-McCarthy, James M. Hogle, Martin Karplus

J. Comput. Aided Mol. Des., 2001

2000

Quantitative Structure-Activity Relationship Studies of Progesterone Receptor Binding Steroids.

Sung-Sau So, Steven P. van Helden, Vincent J. van Geerestein, Martin Karplus

J. Chem. Inf. Comput. Sci., 2000

Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach.

Amedeo Caflisch, Hans J. Schramm, Martin Karplus

J. Comput. Aided Mol. Des., 2000

1999

A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors.

Sung-Sau So, Martin Karplus

J. Comput. Aided Mol. Des., 1999

1997

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

Amedeo Caflisch, Stefan Fischer, Martin Karplus

J. Comput. Chem., 1997

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations.

Christian Bartels, Martin Karplus

J. Comput. Chem., 1997

1996

New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities.

Arnaud Blondel, Martin Karplus

J. Comput. Chem., 1996

Functionality map analysis of the active site cleft of human thrombin.

Peter D. J. Grootenhuis, Martin Karplus

J. Comput. Aided Mol. Des., 1996

1995

Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study.

Benoît Roux, Martin Karplus

J. Comput. Chem., 1995

Harmonic Analysis of Large Systems. III. Comparison with Molecular Dynamics.

Dusanka Janezic, Richard M. Venable, Martin Karplus

J. Comput. Chem., 1995

Harmonic Analysis of Large Systems. II. Comaprison of Different Protein Models.

Dusanka Janezic, Martin Karplus

J. Comput. Chem., 1995

Harmonic Analysis of Large Systems. I. Methodology.

Bernard R. Brooks, Dusanka Janezic, Martin Karplus

J. Comput. Chem., 1995

Thermodynamics and kinetics of protein folding.

Andrej Sali, Eugene I. Shakhnovich, Martin Karplus

Proceedings of the Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995