Scoring docked conformations generated by rigid-body protein-protein docking

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

1983 • 14,615 citations

Physical chemistry of surfaces

1998 • 11,723 citations

Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons

1991 • 5,267 citations

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

1985 • 1,570 citations

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

1992 • 1,062 citations

Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton

1997 • 808 citations

Physical Chemistry of Surfaces

1979 • 787 citations

Determination of atomic desolvation energies from the structures of crystallized proteins

1997 • 540 citations

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction 1 1Edited by F. Cohen

1998 • 450 citations

Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys

1996 • 424 citations

“Soft docking”: Matching of molecular surface cubes

1991 • 402 citations

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5

1989 • 367 citations

Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes

1995 • 345 citations

Calculation of the free energy of association for protein complexes

1992 • 326 citations

Protein docking and complementarity

1991 • 297 citations

BiGGER: A new (soft) docking algorithm for predicting protein interactions

2000 • 290 citations

Use of pair potentials across protein interfaces in screening predicted docked complexes

1999 • 255 citations

Rapid refinement of protein interfaces incorporating solvation: application to the docking problem

1998 • 246 citations

Free Energy Landscapes of Encounter Complexes in Protein-Protein Association

1999 • 195 citations

Hydrophobic docking: A proposed enhancement to molecular recognition techniques

1994 • 191 citations

A geometry-based suite of moleculardocking processes

1995 • 184 citations

A systematic study of low-resolution recognition in protein–protein complexes

1999 • 181 citations

A Continuum Model for Protein–Protein Interactions: Application to the Docking Problem

1995 • 166 citations

Entropy in protein folding and in protein—protein interactions

1997 • 164 citations

Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity

1995 • 154 citations

Examination of shape complementarity in docking ofUnbound proteins

1999 • 152 citations

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

1994 • 150 citations

Protein‐protein recognition analyzed by docking simulation

1991 • 147 citations

Definition of the Interaction Domain for Cytochrome con Cytochrome c Oxidase

1999 • 146 citations

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

1998 • 145 citations

Empirical potentials and functions for protein folding and binding

1997 • 137 citations

Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy

1994 • 132 citations

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model

1998 • 131 citations

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

1995 • 117 citations

Low-resolution docking: Prediction of complexes for underdetermined structures

1998 • 115 citations

Hydrogen Bonding and Molecular Surface Shape Complementarity as a Basis for Protein Docking

1996 • 113 citations

Predictive docking of protein—protein and protein—DNA complexes

1998 • 111 citations

Affinity and Specificity of Serine Endopeptidase-Protein Inhibitor Interactions

1993 • 100 citations

Definition of the Interaction Domain for Cytochrome con Cytochrome c Oxidase

1999 • 99 citations

Prediction of protein complexes using empirical free energy functions

1996 • 98 citations

Docking by least-squares fitting of molecular surface patterns

1992 • 96 citations

Evaluation of the CASP2 docking section

1997 • 94 citations

PUZZLE: A New Method for Automated Protein Docking Based on Surface Shape Complementarity

1994 • 91 citations

A new class of models for computing receptor-ligand binding affinities

1997 • 71 citations

Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions

1996 • 65 citations

Surveying molecular interactions with DOT

1995 • 58 citations

Evaluation of the CASP2 docking section

1997 • 54 citations

Docking enzyme‐inhibitor complexes using a preference‐based free‐energy surface

1996 • 51 citations

Grid‐search molecular accessible surface algorithm for solving the protein docking problem

1991 • 45 citations

Low‐resolution docking: Prediction of complexes for underdetermined structures

1996 • 37 citations

The Fourier-Green's function and the rapid evaluation of molecular potentials

1994 • 33 citations

Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV‐1 protease

1995 • 33 citations

Simple method for locating possible ligand binding sites on protein surfaces

1999 • 32 citations

Rigid‐body docking with mutant constraints of influenza hemagglutinin with antibody HC19

1994 • 30 citations

High resolution fast quantitative docking using fourier domain correlation techniques

1997 • 28 citations

Peptide docking using dynamic programming

1996 • 23 citations

Empirical free energy as a target function in docking and design: application to HIV‐1 protease inhibitors

1996 • 22 citations

Selecting near‐native conformations in homology modeling: The role of molecular mechanics and solvation terms

1998 • 22 citations

Fourier-filtered van der Waals contact surfaces: accurate ligand shapes from protein structures

1997 • 13 citations

Protein docking combining symbolic descriptions of molecular surfaces and grid-based scoring functions.

1995 • 11 citations

Production, characterization and cytotoxic properties of a diphtheria toxin-ciliary neurotrophic factor fusion protein

1995 • 9 citations