Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network

(2012) Simone Daminelli et al.   Integrative Biology

ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures

(2012) Janez Konc et al.   Journal of Chemical Information and Modeling

Use of genome-wide association studies for drug repositioning

(2012) Philippe Sanseau et al.   NATURE BIOTECHNOLOGY

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

(2011) Lei Xie et al.   Annual Review of Pharmacology and Toxicology

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

Molecular complexity and fragment-based drug discovery: ten years on

(2011) Andrew R Leach et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

RP101 (brivudine) binds to heat shock protein HSP27 (HSPB1) and enhances survival in animals and pancreatic cancer patients

(2011) Jörg-Christian Heinrich et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

Probing the links between in vitro potency, ADMET and physicochemical parameters

(2011) M. Paul Gleeson et al.   NATURE REVIEWS DRUG DISCOVERY

Computational Repositioning of the Anticonvulsant Topiramate for Inflammatory Bowel Disease

(2011) J. T. Dudley et al.   Science Translational Medicine

Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs

(2011) Olga V. Kalinina et al.   PLoS Computational Biology

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir

(2011) Li Xie et al.   PLoS Computational Biology

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

(2011) Tianyun Liu et al.   PLoS Computational Biology

Chemoinformatic Analysis of Biologically Active Macrocycles

(2010) Wolfgang Brandt et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

PubChem as a public resource for drug discovery

(2010) Qingliang Li et al.   DRUG DISCOVERY TODAY

The Comparative Toxicogenomics Database: update 2011

(2010) A. P. Davis et al.   NUCLEIC ACIDS RESEARCH

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Unveiling the role of network and systems biology in drug discovery

(2010) Albert Pujol et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

(2010) Sarah L. Kinnings et al.   PLoS Computational Biology

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

(2009) L. Xie et al.   BIOINFORMATICS

Properties and identification of human protein drug targets

(2009) Tala M. Bakheet et al.   BIOINFORMATICS

Pharmacological Promiscuity: Dependence on Compound Properties and Target Specificity in a Set of Recent Roche Compounds

(2009) Jens-Uwe Peters et al.   ChemMedChem

The topology of drug–target interaction networks: implicit dependence on drug properties and target families

(2009) Jordi Mestres et al.   Molecular BioSystems

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

Update of TTD: Therapeutic Target Database

(2009) Feng Zhu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Small Molecule Subgraph Detector (SMSD) toolkit

(2009) Syed Rahman et al.   Journal of Cheminformatics

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

(2009) Li Xie et al.   PLoS Computational Biology

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

(2008) R. Najmanovich et al.   BIOINFORMATICS

Structural Characterization of Myotoxic Ecarpholin S From Echis carinatus Venom

(2008) Xingding Zhou et al.   BIOPHYSICAL JOURNAL

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

(2008) Noel M O'Boyle et al.   Chemistry Central Journal

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

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

Suramin: Clinical Uses and Structure-Activity Relationships

(2008) Ross McGeary et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

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