Thermodynamics and kinetics of protein folding. - Andrej Sali; Eugene I. Shakhnovich; Martin Karplus (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

Harmonic Analysis of Large Systems. I. Methodology. - Bernard R. Brooks; Dusanka Janezic; 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. III. Comparison with Molecular Dynamics. - Dusanka Janezic; Richard M. Venable; Martin Karplus (J. Comput. Chem., 1995)

Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. - Benoît Roux; Martin Karplus (J. Comput. Chem., 1995)

Functionality map analysis of the active site cleft of human thrombin. - Peter D. J. Grootenhuis; Martin Karplus (J. Comput. Aided Mol. Des., 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)

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations. - Christian Bartels; Martin Karplus (J. Comput. Chem., 1997)

Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. - Amedeo Caflisch; Stefan Fischer 004; Martin Karplus (J. Comput. Chem., 1997)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation. - Robert J. Petrella; Martin Karplus (J. Comput. Chem., 2005)

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)

Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements. - Marco Cecchini; Anne Houdusse; Martin Karplus (PLoS Comput. Biol., 2008)

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; et al. (J. Comput. Chem., 2009)

Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning. - Simone Conti; Martin Karplus (PLoS Comput. Biol., 2019)

ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learning. - Simone Conti; Victor Ovchinnikov; Martin Karplus (J. Comput. Chem., 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)

High-throughput molecular simulations of SARS-CoV-2 receptor binding domain mutants quantify correlations between dynamic fluctuations and protein expression. - Victor Ovchinnikov; Martin Karplus (J. Comput. Chem., 2025)