Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations

The Protein Data Bank

2000 • 35,287 citations

Computer Simulation of Liquids

2017 • 20,627 citations

Computer Simulation of Liquids

1988 • 15,963 citations

Numerical recipes in Pascal: the art of scientific computing

1990 • 12,293 citations

R: A Language for Data Analysis and Graphics

1996 • 9,943 citations

R: A Language for Data Analysis and Graphics

1996 • 4,255 citations

Numerical recipes in Fortran (The art of scientific computing)

1993 • 3,845 citations

Solvation energy in protein folding and binding

1986 • 1,853 citations

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions

1997 • 1,403 citations

Simulation of activation free energies in molecular systems

1996 • 1,279 citations

Effective energy function for proteins in solution

1999 • 1,269 citations

Principles of docking: An overview of search algorithms and a guide to scoring functions

2002 • 1,200 citations

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

1992 • 1,062 citations

Numerical recipes in FORTRAN (2nd ed.): the art of scientific computing

1992 • 1,061 citations

Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli

1989 • 989 citations

A simple physical model for binding energy hot spots in protein–protein complexes

2002 • 812 citations

Native protein sequences are close to optimal for their structures

2000 • 811 citations

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

1997 • 808 citations

Bayesian statistical analysis of protein side‐chain rotamer preferences

1997 • 792 citations

CAPRI: A Critical Assessment of PRedicted Interactions

2003 • 664 citations

An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes

2003 • 510 citations

Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis

1997 • 474 citations

Prediction of protein–protein interactions by docking methods

2002 • 453 citations

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1999 • 433 citations

Assessment of blind predictions of protein–protein interactions: Current status of docking methods

2003 • 409 citations

A physicochemical study of protein G, a molecule with unique immunoglobulin G-binding properties.

1986 • 402 citations

Residue frequencies and pairing preferences at protein-protein interfaces

2001 • 383 citations

Docking unbound proteins using shape complementarity, desolvation, and electrostatics

2002 • 367 citations

A protein–protein docking benchmark

2003 • 352 citations

Rosetta in CASP4: Progress in ab initio protein structure prediction

2001 • 310 citations

Protein docking and complementarity

1991 • 297 citations

Protein docking using continuum electrostatics and geometric fit

2001 • 296 citations

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

2000 • 290 citations

A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein.

1995 • 256 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

The Interaction of Bovine Pancreatic Deoxyribonuclease I and Skeletal Muscle Actin

1980 • 205 citations

Soft protein–protein docking in internal coordinates

2002 • 196 citations

Co-evolutionary Analysis Reveals Insights into Protein–Protein Interactions

2002 • 184 citations

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

1999 • 181 citations

Critical assessment of methods of protein structure prediction (CASP): Round IV

2001 • 172 citations

An improved protein decoy set for testing energy functions for protein structure prediction

2003 • 160 citations

Protein docking along smooth association pathways

2001 • 136 citations

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

2000 • 132 citations

Electrostatics in protein–protein docking

2002 • 130 citations

Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tables

1993 • 126 citations

Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis

2001 • 125 citations

Protein–protein association kinetics and protein docking

2002 • 114 citations

The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF·5G9 complex 1 1Edited by D. C. Rees

1998 • 111 citations

Identification of protein oligomerization states by analysis of interface conservation

2001 • 111 citations

Protein–protein docking predictions for the CAPRI experiment

2003 • 104 citations

Fasciculin 2 Binds to the Peripheral Site on Acetylcholinesterase and Inhibits Substrate Hydrolysis by Slowing a Step Involving Proton Transfer during Enzyme Acylation

1995 • 102 citations

Polar and nonpolar atomic environments in the protein core: Implications for folding and binding

1994 • 87 citations

Bovine stefin C, a new member of the stefin family.

1993 • 82 citations

Protein–protein docking with multiple residue conformations and residue substitutions

2002 • 62 citations

Interactions of Cyclins with Cyclin-Dependent Kinases: A Common Interactive Mechanism

1997 • 54 citations

Kinetics and thermodynamics of the interaction of elongation factor Tu with elongation factor Ts, guanine nucleotides, and aminoacyl-tRNA.

1985 • 53 citations

Thermodynamic Investigation of Hirudin Binding to the Slow and Fast Forms of Thrombin: Evidence for Folding Transitions in the Inhibitor and Protease Coupled to Binding

1995 • 44 citations

Binding constants for a physiologic electron-transfer protein complex between methylamine dehydrogenase and amicyanin. Effects of ionic strength and bound copper on binding

1993 • 27 citations

Binding of the Recombinant Proteinase Inhibitor Eglin C from LeechHzrudo Medzcznalzsto Human Leukocyte Elastase, Bovine α-Chymotrypsin and Subtilisin Carlsberg: Thermodynamic Study

1988 • 25 citations

Analysis of binding properties between 20 kDa human growth hormone (hGH) and hGH receptor (hGHR): the binding affinity for hGHR extracellular domain and mode of receptor dimerization

1999 • 24 citations

Cation-Promoted Association of Escherichia coli Phosphocarrier Protein IIA^Glc with Regulatory Target Protein Glycerol Kinase: Substitutions of a Zinc(II) Ligand and Implications for Inducer Exclusion

1998 • 17 citations

Binding of the bovine pancreatic secretory trypsin inhibitor (Kazal) to bovine serine (pro)enzymes

1987 • 11 citations

SOFTDOCK: understanding of molecular recognition through a systematic docking study

2002 • 11 citations