Martin Karplus

Publication Activity (10 Years)

Years Active: 1995-2022
Publications (10 Years): 3

Top Topics

Protein Interaction

Machine Learning

Clonal Selection Algorithm

Top Venues

PLoS Comput. Biol.

J. Comput. Chem.

Publications

Simone Conti, Victor Ovchinnikov, Jonathan G. Faris, Arup K. Chakraborty, Martin Karplus, Kayla G. Sprenger
Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV. PLoS Comput. Biol. 18 (4) (2022)
Simone Conti, Victor Ovchinnikov, Martin Karplus
ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning. J. Comput. Chem. 43 (25) (2022)
Simone Conti, Martin Karplus
Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning. PLoS Comput. Biol. 15 (4) (2019)
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, V. 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
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Marco Cecchini, A. Houdusse, Martin Karplus
Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements. PLoS Comput. Biol. 4 (8) (2008)
Erik Evensen, Diane Joseph-McCarthy, Gregory A. Weiss, Stuart L. Schreiber, Martin Karplus
Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. J. Comput. Aided Mol. Des. 21 (7) (2007)
Robert J. Petrella, Martin Karplus
Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation. J. Comput. Chem. 26 (8) (2005)
Marcus Elstner, Qiang Cui, Petra Munih, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus
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. 24 (5) (2003)
Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. J. Comput. Chem. 24 (2) (2003)
Vincent Zoete, Olivier Michielin, Martin Karplus
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. J. Comput. Aided Mol. Des. 17 (12) (2003)
Michael Schaefer, Christian Bartels, Fabrice Leclerc, Martin Karplus
Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. J. Comput. Chem. 22 (15) (2001)
Ryan Bitetti-Putzer, Diane Joseph-McCarthy, James M. Hogle, Martin Karplus
Functional group placement in protein binding sites: a comparison of GRID and MCSS. J. Comput. Aided Mol. Des. 15 (10) (2001)
Sung-Sau So, Martin Karplus
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. 15 (7) (2001)
Amedeo Caflisch, Hans J. Schramm, Martin Karplus
Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. J. Comput. Aided Mol. Des. 14 (2) (2000)
Sung-Sau So, Steven P. van Helden, Vincent J. van Geerestein, Martin Karplus
Quantitative Structure-Activity Relationship Studies of Progesterone Receptor Binding Steroids. J. Chem. Inf. Comput. Sci. 40 (3) (2000)
Sung-Sau So, Martin Karplus
A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J. Comput. Aided Mol. Des. 13 (3) (1999)
Amedeo Caflisch, Stefan Fischer, Martin Karplus
Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. J. Comput. Chem. 18 (6) (1997)
Christian Bartels, Martin Karplus
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations. J. Comput. Chem. 18 (12) (1997)
Peter D. J. Grootenhuis, Martin Karplus
Functionality map analysis of the active site cleft of human thrombin. J. Comput. Aided Mol. Des. 10 (1) (1996)
Arnaud Blondel, Martin Karplus
New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities. J. Comput. Chem. 17 (9) (1996)
Benoît Roux, Martin Karplus
Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. J. Comput. Chem. 16 (6) (1995)
Andrej Sali, Eugene I. Shakhnovich, Martin Karplus
Thermodynamics and kinetics of protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding (1995)
Dusanka Janezic, Martin Karplus
Harmonic Analysis of Large Systems. II. Comaprison of Different Protein Models. J. Comput. Chem. 16 (12) (1995)
Bernard R. Brooks, Dusanka Janezic, Martin Karplus
Harmonic Analysis of Large Systems. I. Methodology. J. Comput. Chem. 16 (12) (1995)
Dusanka Janezic, Richard M. Venable, Martin Karplus
Harmonic Analysis of Large Systems. III. Comparison with Molecular Dynamics. J. Comput. Chem. 16 (12) (1995)