Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects

A novel frameshift mutation in KCNQ4 in a family with autosomal recessive non-syndromic hearing loss

(2015) Koichiro Wasano et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

(2015) Francis Gaudreault et al.   BIOINFORMATICS

PDID: database of molecular-level putative protein–drug interactions in the structural human proteome

(2015) Chen Wang et al.   BIOINFORMATICS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Detection of Binding Site Molecular Interaction Field Similarities

(2015) Matthieu Chartier et al.   Journal of Chemical Information and Modeling

FlexAID: Revisiting Docking on Non-Native-Complex Structures

(2015) Francis Gaudreault et al.   Journal of Chemical Information and Modeling

The SIDER database of drugs and side effects

(2015) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

Achievements and challenges in structural bioinformatics and computational biophysics

(2014) I. Samish et al.   BIOINFORMATICS

Discovery of 6-[5-(4-fluorophenyl)-3-methyl-pyrazol-4-yl]-benzoxazin-3-one derivatives as novel selective nonsteroidal mineralocorticoid receptor antagonists

(2014) Tomoaki Hasui et al.   BIOORGANIC & MEDICINAL CHEMISTRY

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

(2014) Mathieu Larocque et al.   BMC Systems Biology

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Contributions of Molecular Properties to Drug Promiscuity

(2013) Ákos Tarcsay et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of Similar Binding Sites to Detect Distant Polypharmacology

(2013) Xavier Jalencas et al.   Molecular Informatics

The Rice Bacterial PathogenXanthomonas oryzaepv.oryzaeProduces 3-Hydroxybenzoic Acid and 4-Hydroxybenzoic Acid via XanB2 for Use in Xanthomonadin, Ubiquinone, and Exopolysaccharide Biosynthesis

(2013) Lian Zhou et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users

(2012) Ana Rath et al.   HUMAN MUTATION

Gene Ontology Annotations and Resources

(2012)   NUCLEIC ACIDS RESEARCH

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

(2012) Marija Milacic et al.   Cancers

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins

(2011) J. Meslamani et al.   BIOINFORMATICS

Structural Chemistry of the Histone Methyltransferases Cofactor Binding Site

(2011) Valérie Campagna-Slater et al.   Journal of Chemical Information and Modeling

A Strategy for Antagonizing Quorum Sensing

(2011) Guozhou Chen et al.   MOLECULAR CELL

Comprehensive analysis of kinase inhibitor selectivity

(2011) Mindy I Davis et al.   NATURE BIOTECHNOLOGY

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

(2010) Gye Won Han et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

(2009) Constantina Bakolitsa et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

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

Structural basis for the binding of naproxen to human serum albumin in the presence of fatty acids and the GA module

(2008) Sara Lejon et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

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

(2008) R. Najmanovich et al.   BIOINFORMATICS

PDTD: a web-accessible protein database for drug target identification

(2008) Zhenting Gao et al.   BMC BIOINFORMATICS

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

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE