Chemogenomics in drug discovery: computational methods based on the comparison of binding sites

Functional Prediction of Binding Pockets

(2012) Maria Kontoyianni et al.   Journal of Chemical Information and Modeling

Fragment screening to predict druggability (ligandability) and lead discovery success

(2011) Fredrik N.B. Edfeldt et al.   DRUG DISCOVERY TODAY

Computational tools for polypharmacology and repurposing

(2011) Janosch Achenbach et al.   Future Medicinal Chemistry

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

Fragment Based Drug Discovery: Practical Implementation Based on 19F NMR Spectroscopy

(2011) John B. Jordan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Large-Scale Evaluation of CavBase for Analyzing the Polypharmacology of Kinase Inhibitors

(2011) Tuomo Kalliokoski et al.   Molecular Informatics

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

PoSSuM: a database of similar protein-ligand binding and putative pockets

(2011) J.-I. Ito et al.   NUCLEIC ACIDS RESEARCH

Cofactor-binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space

(2011) Björn Stegemann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets

(2010) Hongbo Zhu et al.   BIOINFORMATICS

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

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

Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe

(2010) Francesca Milletti et al.   Journal of Chemical Information and Modeling

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites

(2010) Nathanaël Weill et al.   Journal of Chemical Information and Modeling

Large-Scale Comparison of Four Binding Site Detection Algorithms

(2010) Peter Schmidtke et al.   Journal of Chemical Information and Modeling

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets

(2010) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

Drug-like Density: A Method of Quantifying the “Bindability” of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank

(2010) Robert P. Sheridan et al.   Journal of Chemical Information and Modeling

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

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

Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements

(2010) Enrico De Franchi et al.   PLoS One

Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments

(2010) Anna Vulpetti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation

(2009) I. Wallach et al.   BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family

(2009) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

Identifying and Characterizing Binding Sites and Assessing Druggability

(2009) Thomas A. Halgren   Journal of Chemical Information and Modeling

Selectively Nonselective Kinase Inhibition: Striking the Right Balance

(2009) Richard Morphy   JOURNAL OF MEDICINAL CHEMISTRY

Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine

(2009) Anna Vulpetti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Mechanisms of drug combinations: interaction and network perspectives

(2009) Jia Jia et al.   NATURE REVIEWS DRUG DISCOVERY

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

ATP competitive inhibitors of d-alanine–d-alanine ligase based on protein kinase inhibitor scaffolds

(2008) Gemma Triola et al.   BIOORGANIC & MEDICINAL CHEMISTRY

How to Measure the Similarity Between Protein Ligand-Binding Sites?

(2008) Esther Kellenberger et al.   Current Computer-Aided Drug Design

Data completeness—the Achilles heel of drug-target networks

(2008) Jordi Mestres et al.   NATURE BIOTECHNOLOGY

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple and fuzzy method to align and compare druggable ligand-binding sites

(2008) Claire Schalon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions

(2008) Ryoichi Minai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS