Predicting protein targets for drug-like compounds using transcriptomics

Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge

(2016) Zhaofeng Ye et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Direct small-molecule inhibitors of KRAS: from structural insights to mechanism-based design

(2016) Jonathan M. L. Ostrem et al.   NATURE REVIEWS DRUG DISCOVERY

A CHIPotle in physiology and disease

(2015) Indranil Paul et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment

(2015) Matthew P. Baumgartner et al.   Journal of Chemical Information and Modeling

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool

(2015) David Ryan Koes et al.   PLoS One

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Drug target prioritization by perturbed gene expression and network information

(2015) Zerrin Isik et al.   Scientific Reports

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

(2015) Yu-Chen Lo et al.   PLoS Computational Biology

Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze

(2015) Francisco Martínez-Jiménez et al.   PLoS Computational Biology

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

(2014) David Gfeller et al.   NUCLEIC ACIDS RESEARCH

SuperPred: update on drug classification and target prediction

(2014) Janette Nickel et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Finding the targets of a drug by integration of gene expression data with a protein interaction network

(2013) Griet Laenen et al.   Molecular BioSystems

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling

(2012) Jamel Meslamani et al.   Journal of Chemical Information and Modeling

ZINCPharmer: pharmacophore search of the ZINC database

(2012) D. R. Koes et al.   NUCLEIC ACIDS RESEARCH

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach

(2012) Jui-Chih Wang et al.   NUCLEIC ACIDS RESEARCH

Identifying mechanism-of-action targets for drugs and probes

(2012) E. Gregori-Puigjane et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

(2012) T. Maurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Too many roads not taken

(2011) Aled M. Edwards et al.   NATURE

How were new medicines discovered?

(2011) David C. Swinney et al.   NATURE REVIEWS DRUG DISCOVERY

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

(2010) Y. Yamanishi et al.   BIOINFORMATICS

Structure-Based Approaches to Target Fishing and Ligand Profiling

(2010) Didier Rognan   Molecular Informatics

The (un)targeted cancer kinome

(2010) Oleg Fedorov et al.   Nature Chemical Biology

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS

PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

(2010) Xiaofeng Liu et al.   NUCLEIC ACIDS RESEARCH

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel modulation factor quantifies the role of water molecules in protein interactions

(2010) Marta Bueno et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Regulation of 3-Phosphoinositide-Dependent Protein Kinase 1 Activity by Homodimerization in Live Cells

(2010) T. A. Masters et al.   Science Signaling

Novel trends in high-throughput screening

(2009) Lorenz M Mayr et al.   CURRENT OPINION IN PHARMACOLOGY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia

(2008) Elissa J. Cosgrove et al.   BIOINFORMATICS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Kinase requirements in human cells: I. Comparing kinase requirements across various cell types

(2008) D. A. Grueneberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA