A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites

The quickhull algorithm for convex hulls

1996 • 4,965 citations

Classical Electrostatics in Biology and Chemistry

1995 • 2,801 citations

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

2006 • 1,686 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

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

2005 • 1,013 citations

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

1995 • 979 citations

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

1997 • 683 citations

Analysis of protein-protein interaction sites using surface patches 1 1Edited by G.Von Heijne

1997 • 607 citations

Fast prediction and visualization of protein binding pockets with PASS.

2000 • 521 citations

Network Analysis of Protein Structures Identifies Functional Residues

2004 • 487 citations

Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes

2005 • 397 citations

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

2004 • 343 citations

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

1992 • 318 citations

Predicting protein function from sequence and structural data

2005 • 310 citations

On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites

2006 • 277 citations

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

1996 • 246 citations

A method for localizing ligand binding pockets in protein structures

2005 • 216 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

Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding

2004 • 164 citations

How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

2006 • 133 citations

Comprehensive identification of "druggable" protein ligand binding sites.

2004 • 116 citations

Accounting for global protein deformability during protein–protein and protein–ligand docking

2005 • 101 citations

Extreme Elevation on a 2-Manifold

2006 • 95 citations

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

2001 • 94 citations

Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding

2006 • 84 citations

Identification of Substrate Binding Sites in Enzymes by Computational Solvent Mapping

2003 • 73 citations

Predicting protein functional sites with phylogenetic motifs

2004 • 73 citations

In silico identification of functional regions in proteins

2005 • 57 citations

Looking at Enzymes from the Inside out: The Proximity of Catalytic Residues to the Molecular Centroid can be used for Detection of Active Sites and Enzyme–Ligand Interfaces

2005 • 56 citations

Identification of Ligand Binding Sites on Proteins Using a Multi-Scale Approach

2002 • 44 citations

Classification of Chemical Compounds by Protein−Compound Docking for Use in Designing a Focused Library

2005 • 40 citations

COARSE AND RELIABLE GEOMETRIC ALIGNMENT FOR PROTEIN DOCKING

2004 • 35 citations

An intuitive approach to measuring protein surface curvature

2005 • 34 citations

Simple method for locating possible ligand binding sites on protein surfaces

1999 • 32 citations

A New Method for Estimating the Importance of Hydrophobic Groups in the Binding Site of a Protein

2005 • 25 citations

Small Molecule Recognition: Solid Angles Surface Representation and Molecular Shape Complementarity

1999 • 22 citations

Surface solid angle-based site points for molecular docking.

1998 • 18 citations

A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein.

2003 • 9 citations

A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening

2006 • 9 citations