Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features

Binding site comparison for function prediction and pharmaceutical discovery

(2013) Janez Konc et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

(2013) Nickolay A. Khazanov et al.   PLoS Computational Biology

Pocket-Based Drug Design: Exploring Pocket Space

(2012) Xiliang Zheng et al.   AAPS Journal

BioJava: an open-source framework for bioinformatics in 2012

(2012) A. Prlic et al.   BIOINFORMATICS

Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes

(2012) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins

(2012) Sebastian Schneider et al.   JOURNAL OF STRUCTURAL BIOLOGY

Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement

(2012) Ambrish Roy et al.   STRUCTURE

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction

(2011) Z. Zhang et al.   BIOINFORMATICS

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

(2011) Peter Schmidtke et al.   BIOINFORMATICS

Structure-based systems biology for analyzing off-target binding

(2011) Lei Xie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-based computational analysis of protein binding sites for function and druggability prediction

(2011) Britta Nisius et al.   JOURNAL OF BIOTECHNOLOGY

DrugPred: A Structure-Based Approach To Predict Protein Druggability Developed Using an Extensive Nonredundant Data Set

(2011) Agata Krasowski et al.   Journal of Chemical Information and Modeling

Exploiting a Reduced Set of Weighted Average Features to Improve Prediction of DNA-Binding Residues from 3D Structures

(2011) Yi Xiong et al.   PLoS One

A Critical Comparative Assessment of Predictions of Protein-Binding Sites for Biologically Relevant Organic Compounds

(2011) Ke Chen et al.   STRUCTURE

In Silico Prediction of Binding Sites on Proteins

(2010) Simon Leis et al.   CURRENT MEDICINAL CHEMISTRY

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

EasyMIFs and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures

(2009) Dario Ghersi et al.   BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

FINDSITE: a combined evolution/structure-based approach to protein function prediction

(2009) J. Skolnick et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

(2009) Mile Šikić et al.   PLoS Computational Biology

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

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

Predicting small ligand binding sites in proteins using backbone structure

(2008) Andrew J. Bordner   BIOINFORMATICS

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures

(2008) Mizuki Morita et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS