Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

(2010) Brice Hoffmann et al.   BMC BIOINFORMATICS

Protein Pockets: Inventory, Shape, and Comparison

(2010) Ryan G. Coleman et al.   Journal of Chemical Information and Modeling

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

(2009) Bingding Huang   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Detection of multiscale pockets on protein surfaces using mathematical morphology

(2009) Takeshi Kawabata   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comprehensive Structural Classification of Ligand-Binding Motifs in Proteins

(2009) Akira R. Kinjo et al.   STRUCTURE

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Two ‘Golden Ratio’ indices in fragment-based drug discovery

(2008) Masaya Orita et al.   DRUG DISCOVERY TODAY

Beyond Picomolar Affinities: Quantitative Aspects of Noncovalent and Covalent Binding of Drugs to Proteins

(2008) Adam J. T. Smith et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fast dynamics perturbation analysis for prediction of protein functional sites

(2008) Dengming Ming et al.   BMC STRUCTURAL BIOLOGY

Pocket extraction on proteins via the Voronoi diagram of spheres

(2007) Donguk Kim et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins

(2007) Yeturu Kalidas et al.   JOURNAL OF STRUCTURAL BIOLOGY

A computational method for the analysis and prediction of protein:phosphopeptide-binding sites

(2004) Brian A. Joughin et al.   PROTEIN SCIENCE