STITCH 4: integration of protein–chemical interactions with user data

Automated QuantMap for rapid quantitative molecular network topology analysis

(2013) Wesley Schaal et al.   BIOINFORMATICS

Analysis of Chemical and Biological Features Yields Mechanistic Insights into Drug Side Effects

(2013) Miquel Duran-Frigola et al.   CHEMISTRY & BIOLOGY

Network-based target ranking for polypharmacological therapies

(2013) Francesca Vitali et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Predicting drug–target interactions through integrative analysis of chemogenetic assays in yeast

(2013) Marja A. Heiskanen et al.   Molecular BioSystems

Towards the Next Generation of Computational Chemogenomics Tools

(2013) D. Rognan   Molecular Informatics

Systematic identification of proteins that elicit drug side effects

(2013) M. Kuhn et al.   Molecular Systems Biology

ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes—now with human data

(2013) Omer Basha et al.   NUCLEIC ACIDS RESEARCH

Comparison of Random Forest and Pipeline Pilot Naïve Bayes in Prospective QSAR Predictions

(2012) Bin Chen et al.   Journal of Chemical Information and Modeling

Large-scale prediction and testing of drug activity on side-effect targets

(2012) Eugen Lounkine et al.   NATURE

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

The Comparative Toxicogenomics Database: update 2013

(2012) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity

(2011) Theonie Anastassiadis et al.   NATURE BIOTECHNOLOGY

Comprehensive analysis of kinase inhibitor selectivity

(2011) Mindy I Davis et al.   NATURE BIOTECHNOLOGY

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

STITCH 3: zooming in on protein-chemical interactions

(2011) M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

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

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

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

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

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Selection of representative protein data sets

(2010) Uwe Hobohm et al.   PROTEIN SCIENCE

Drug-Induced Regulation of Target Expression

(2010) Murat Iskar et al.   PLoS Computational Biology

STITCH 2: an interaction network database for small molecules and proteins

(2009) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

McKusick's Online Mendelian Inheritance in Man (OMIM(R))

(2008) J. Amberger et al.   NUCLEIC ACIDS RESEARCH