Drug–target interaction prediction: databases, web servers and computational models

Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data

(2015) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Predicting Drug-Target Interactions via Within-Score and Between-Score

(2015) Jian-Yu Shi et al.   Biomed Research International

Toward more realistic drug-target interaction predictions

(2014) T. Pahikkala et al.   BRIEFINGS IN BIOINFORMATICS

Screening drug target proteins based on sequence information

(2014) Jiao T. Wang et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Computational Prediction of DrugTarget Interactions Using Chemical, Biological, and Network Features

(2014) Dong-Sheng Cao et al.   Molecular Informatics

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

DINIES: drug–target interaction network inference engine based on supervised analysis

(2014) Yoshihiro Yamanishi et al.   NUCLEIC ACIDS RESEARCH

ASDCD: Antifungal Synergistic Drug Combination Database

(2014) Xing Chen et al.   PLoS One

Drug target inference through pathway analysis of genomics data

(2013) Haisu Ma et al.   ADVANCED DRUG DELIVERY REVIEWS

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Novel human lncRNA–disease association inference based on lncRNA expression profiles

(2013) Xing Chen et al.   BIOINFORMATICS

Similarity-based machine learning methods for predicting drug–target interactions: a brief review

(2013) Hao Ding et al.   BRIEFINGS IN BIOINFORMATICS

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

(2013) Murat Can Cobanoglu et al.   Journal of Chemical Information and Modeling

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands

(2013) Adam J. Pawson et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2014: a resource for targeted therapeutics

(2013) Chu Qin et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

A Semi-Supervised Method for Drug-Target Interaction Prediction with Consistency in Networks

(2013) Hailin Chen et al.   PLoS One

Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach

(2013) Dorothea Emig et al.   PLoS One

Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks

(2013) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance

(2013) Edwin Wang et al.   SEMINARS IN CANCER BIOLOGY

CancerDR: Cancer Drug Resistance Database

(2013) Rahul Kumar et al.   Scientific Reports

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

Flaws in evaluation schemes for pair-input computational predictions

(2012) Yungki Park et al.   NATURE METHODS

A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data

(2012) Hua Yu et al.   PLoS One

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Strategies to Discover Unexpected Targets for Drugs Active at G Protein–Coupled Receptors

(2011) John A. Allen et al.   Annual Review of Pharmacology and Toxicology

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

Drug discovery in the age of systems biology: the rise of computational approaches for data integration

(2011) Murat Iskar et al.   CURRENT OPINION IN BIOTECHNOLOGY

Target–drug interactions: first principles and their application to drug discovery

(2011) Sara Núñez et al.   DRUG DISCOVERY TODAY

Proteomics applied to exercise physiology: A cutting-edge technology

(2011) Bernardo A. Petriz et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Comprehensive analysis of kinase inhibitor selectivity

(2011) Mindy I Davis et al.   NATURE BIOTECHNOLOGY

Navigating the kinome

(2011) James T Metz et al.   Nature Chemical Biology

canSAR: an integrated cancer public translational research and drug discovery resource

(2011) Mark D. Halling-Brown et al.   NUCLEIC ACIDS RESEARCH

SuperTarget goes quantitative: update on drug-target interactions

(2011) N. Hecker et al.   NUCLEIC ACIDS RESEARCH

TDR Targets: a chemogenomics resource for neglected diseases

(2011) M. P. Magarinos et al.   NUCLEIC ACIDS RESEARCH

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

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

(2010) Zheng Xia et al.   BMC Systems Biology

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

Database resources of the National Center for Biotechnology Information

(2010) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Functional association between influenza A (H1N1) virus and human

(2009) Tao Huang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

DCDB: Drug combination database

(2009) Y. Liu et al.   BIOINFORMATICS

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

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

(2008) Zhenting Gao et al.   BMC BIOINFORMATICS

From Single- to Multi-Target Drugs in Cancer Therapy: When Aspecificity Becomes an Advantage

(2008) S. Giordano et al.   CURRENT MEDICINAL CHEMISTRY

Drugs and their molecular targets: an updated overview

(2008) Yves Landry et al.   FUNDAMENTAL & CLINICAL PHARMACOLOGY

The prediction of interferon treatment effects based on time series microarray gene expression profiles

(2008) Tao Huang et al.   Journal of Translational Medicine

Finding multiple target optimal intervention in disease-related molecular network

(2008) Kun Yang et al.   Molecular Systems Biology

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE