Progress in Modeling of Protein Structures and Interactions

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1997 • 71,835 citations

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

1983 • 14,615 citations

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1995 • 12,826 citations

Principles that Govern the Folding of Protein Chains

1973 • 6,771 citations

Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne

1999 • 5,382 citations

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

2003 • 2,893 citations

Molecular dynamics simulations of biomolecules

2002 • 2,845 citations

Funnels, pathways, and the energy landscape of protein folding: A synthesis

1995 • 2,607 citations

A hierarchical approach to all‐atom protein loop prediction

2004 • 2,190 citations

[20] VERIFY3D: Assessment of protein models with three-dimensional profiles

1997 • 2,048 citations

Force Fields for Protein Simulations

2003 • 1,826 citations

Protein Structure Prediction Using Rosetta

2004 • 1,707 citations

Modeller: Generation and Refinement of Homology-Based Protein Structure Models

2003 • 1,660 citations

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

2003 • 1,619 citations

Tertiary templates for proteins

1987 • 1,485 citations

Monte Carlo-minimization approach to the multiple-minima problem in protein folding.

1987 • 1,419 citations

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

1997 • 1,403 citations

Effective energy function for proteins in solution

1999 • 1,269 citations

Theory of protein folding

2004 • 1,262 citations

Empirical force fields for biological macromolecules: Overview and issues

2004 • 1,231 citations

De Novo Protein Design: Fully Automated Sequence Selection

1997 • 1,129 citations

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

1992 • 1,062 citations

A graph‐theory algorithm for rapid protein side‐chain prediction

2003 • 1,008 citations

Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins

1994 • 954 citations

Toward High-Resolution de Novo Structure Prediction for Small Proteins

2005 • 875 citations

Computational design of receptor and sensor proteins with novel functions

2003 • 665 citations

CAPRI: A Critical Assessment of PRedicted Interactions

2003 • 664 citations

Recent advances in the development and application of implicit solvent models in biomolecule simulations

2004 • 563 citations

Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substitutions

1990 • 485 citations

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction

2005 • 480 citations

Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA

1998 • 464 citations

High-Resolution Protein Design with Backbone Freedom

1998 • 457 citations

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

1996 • 424 citations

Contribution of hydrophobic interactions to protein stability

1988 • 413 citations

Enzyme-like proteins by computational design

2001 • 404 citations

ProTherm, version 4.0: thermodynamic database for proteins and mutants

2003 • 359 citations

Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures

2005 • 341 citations

De novo design of catalytic proteins

2004 • 299 citations

Computational Design of a Biologically Active Enzyme

2004 • 295 citations

Evaluation of Backbone Proton Positions and Dynamics in a Small Protein by Liquid Crystal NMR Spectroscopy

2003 • 294 citations

Computational redesign of protein-protein interaction specificity

2004 • 294 citations

Studies on Protein Stability With T4 Lysozyme

1995 • 291 citations

New Monte Carlo algorithms for protein folding

1999 • 286 citations

Cellulosome assembly revealed by the crystal structure of the cohesin–dockerin complex

2003 • 249 citations

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

2004 • 247 citations

Computational design of protein–protein interactions

2004 • 236 citations

Design, Activity, and Structure of a Highly Specific Artificial Endonuclease

2002 • 232 citations

Energy functions for protein design

1999 • 214 citations

Protein Flexibility and Adaptability Seen in 25 Crystal Forms of T4 Lysozyme

1995 • 193 citations

Realistic protein–protein association rates from a simple diffusional model neglecting long‐range interactions, free energy barriers, and landscape ruggedness

2004 • 191 citations

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.

1994 • 172 citations

Assessment of homology-based predictions in CASP5

2003 • 171 citations

Assessing predictions of protein–protein interaction: The CAPRI experiment

2005 • 159 citations

Scoring profile‐to‐profile sequence alignments

2004 • 135 citations

The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure

2005 • 122 citations

Modulating Calmodulin Binding Specificity through Computational Protein Design

2002 • 117 citations

Conformational sampling for the impatient

2004 • 108 citations

Methods to study protein folding by stopped-flow FT-IR

2004 • 103 citations

Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility

2005 • 101 citations

Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein

2004 • 88 citations

Assembling novel protein folds from super-secondary structural fragments

2003 • 78 citations

TOUCHSTONE: A unified approach to protein structure prediction

2003 • 75 citations

Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments

2003 • 25 citations

Modeling and Studying Proteins with Molecular Dynamics

2004 • 8 citations