Published in BMC Struct Biol on July 19, 2014
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics (2005) 34.83
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68
Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol (1990) 17.64
Solvent-accessible surfaces of proteins and nucleic acids. Science (1983) 11.29
Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr D Biol Crystallogr (1994) 7.53
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci (1998) 7.03
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics (2005) 6.82
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph (1995) 6.64
Template-based modeling and free modeling by I-TASSER in CASP7. Proteins (2007) 6.45
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model (1997) 3.59
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol (2006) 3.54
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci (1997) 3.50
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci (2003) 2.98
Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des (2000) 2.84
Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83
POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph (1992) 2.57
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol (2007) 2.13
The catalytic triad of serine peptidases. Cell Mol Life Sci (2005) 1.82
Ligand binding: functional site location, similarity and docking. Curr Opin Struct Biol (2003) 1.78
The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J Mol Biol (1996) 1.71
Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci U S A (2002) 1.56
Ligand docking and structure-based virtual screening in drug discovery. Curr Top Med Chem (2007) 1.53
Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J Mol Biol (1998) 1.46
Automatic identification and representation of protein binding sites for molecular docking. Protein Sci (1997) 1.43
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
Characterization of local geometry of protein surfaces with the visibility criterion. Proteins (2008) 1.39
Cavity search: an algorithm for the isolation and display of cavity-like binding regions. J Comput Aided Mol Des (1990) 1.31
Travel depth, a new shape descriptor for macromolecules: application to ligand binding. J Mol Biol (2006) 1.24
QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock). Proteins (2000) 1.13
Predictive models for protein crystallization. Methods (2004) 1.08
Structure-based drug design strategies in medicinal chemistry. Curr Top Med Chem (2009) 1.05
Approximation and characterization of molecular surfaces. Biopolymers (1993) 1.03
Structural characterization of proteins using residue environments. Proteins (2005) 1.02
Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmaco (2002) 0.95
Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory. J Comput Chem (2002) 0.92
SuperStar: improved knowledge-based interaction fields for protein binding sites. J Mol Biol (2001) 0.88
Docking-based virtual screening: recent developments. Comb Chem High Throughput Screen (2009) 0.88
Comparative modeling: the state of the art and protein drug target structure prediction. Comb Chem High Throughput Screen (2011) 0.88
Identification of ligand binding sites on proteins using a multi-scale approach. J Am Chem Soc (2002) 0.86
Theoretical and practical considerations in virtual screening: a beaten field? Curr Med Chem (2008) 0.84
Improved mapping of protein binding sites. J Comput Aided Mol Des (2003) 0.81