Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

The Protein Data Bank

2000 • 35,287 citations

SCOP: A structural classification of proteins database for the investigation of sequences and structures

1995 • 6,372 citations

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

1985 • 2,597 citations

An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families

1996 • 1,214 citations

Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design

1998 • 1,017 citations

SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions

1995 • 979 citations

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

2002 • 967 citations

Detection, delineation, measurement and display of cavities in macromolecular structures

1994 • 964 citations

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

1997 • 683 citations

Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

1996 • 585 citations

Progress in Clinical and Biological Research

1989 • 568 citations

PQS: a protein quaternary structure file server

1998 • 547 citations

Untitled

1995 • 545 citations

Functionality maps of binding sites: A multiple copy simultaneous search method

1991 • 535 citations

Fast prediction and visualization of protein binding pockets with PASS.

2000 • 521 citations

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

2001 • 481 citations

A new test set for validating predictions of protein–ligand interaction

2002 • 429 citations

A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology

2002 • 419 citations

Protein clefts in molecular recognition and function.

1996 • 412 citations

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

1997 • 330 citations

POCKET: A computer graphies method for identifying and displaying protein cavities and their surrounding amino acids

1992 • 318 citations

The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria

1996 • 246 citations

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

1998 • 246 citations

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking

2001 • 240 citations

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins11Edited by J. Thornton

2001 • 231 citations

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

1993 • 221 citations

A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures

1994 • 217 citations

Automatic identification and representation of protein binding sites for molecular docking

1997 • 197 citations

Ligand binding: functional site location, similarity and docking

2003 • 194 citations

The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30–>Met variant to 1.7-A resolution.

1993 • 176 citations

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures

2003 • 171 citations

Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases

1994 • 163 citations

E-MSD: an integrated data resource for bioinformatics

2003 • 156 citations

The role of hydrogen-bonds in drug binding.

1989 • 149 citations

The Cyclization Mechanism of Cyclodextrin Glycosyltransferase (CGTase) as Revealed by a γ-Cyclodextrin-CGTase Complex at 1.8-Å Resolution

1999 • 127 citations

Databases for Protein–Ligand Complexes

1998 • 110 citations

Cavity search: An algorithm for the isolation and display of cavity-like binding regions

1990 • 107 citations

Crystal Structures of Soybean .beta.-Amylase Reacted with .beta.-Maltose and Maltal: Active Site Components and Their Apparent Roles in Catalysis

1994 • 100 citations

Superstar: improved knowledge-based interaction fields for protein binding sites11Edited by R. Huber

2001 • 94 citations

Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis.

1994 • 94 citations

Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping

2003 • 73 citations

Recent advances inde novo design strategy for practical lead identification

2003 • 63 citations

Enzyme/Non-enzyme Discrimination and Prediction of Enzyme Active Site Location Using Charge-based Methods

2004 • 56 citations

A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I) Search for pocket regions

1993 • 46 citations

Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere

1995 • 46 citations

Finding and filling protein cavities using cellular logic operations

1992 • 46 citations

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space.

2002 • 39 citations

Modern computational chemistry and drug discovery: structure generating programs

1997 • 38 citations

Time-efficient docking of flexible ligands into active sites of proteins.

1995 • 37 citations

Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations

1995 • 35 citations