Toward more realistic drug-target interaction predictions

Network Pharmacology Strategies Toward Multi-Target Anticancer Therapies: From Computational Models to Experimental Design Principles

(2014) Jing Tang et al.   CURRENT PHARMACEUTICAL DESIGN

Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

(2014) Jing Tang et al.   Journal of Chemical Information and Modeling

Network predicting drug’s anatomical therapeutic chemical code

(2013) Yong-Cui Wang et al.   BIOINFORMATICS

Shaping the interaction landscape of bioactive molecules

(2013) David Gfeller et al.   BIOINFORMATICS

Efficient regularized least-squares algorithms for conditional ranking on relational data

(2013) Tapio Pahikkala et al.   MACHINE LEARNING

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

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

Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

(2013) Michael P. Menden et al.   PLoS One

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations

(2012) Tapio Pahikkala et al.   Algorithms for Molecular Biology

COPICAT: a software system for predicting interactions between proteins and chemical compounds

(2012) Y. Sakakibara et al.   BIOINFORMATICS

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

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

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

Predicting new molecular targets for rhein using network pharmacology

(2012) Aihua Zhang et al.   BMC Systems Biology

Efficient cross-validation for kernelized least-squares regression with sparse basis expansions

(2012) Tapio Pahikkala et al.   MACHINE LEARNING

Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods

(2012) Feixiong Cheng 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

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

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

Kernel-based data fusion improves the drug–protein interaction prediction

(2011) Yong-Cui Wang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Combining Drug and Gene Similarity Measures for Drug-Target Elucidation

(2011) Liat Perlman et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

From in silico target prediction to multi-target drug design: Current databases, methods and applications

(2011) Alexios Koutsoukas et al.   Journal of Proteomics

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

ChEMBL: a large-scale bioactivity database for drug discovery

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

A Computational Approach to Finding Novel Targets for Existing Drugs

(2011) Yvonne Y. Li et al.   PLoS Computational Biology

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

(2010) Y. Yamanishi et al.   BIOINFORMATICS

An experimental comparison of cross-validation techniques for estimating the area under the ROC curve

(2010) Antti Airola et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Biochemical network-based drug-target prediction

(2010) Edda Klipp et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pitfalls of supervised feature selection

(2009) Pawel Smialowski et al.   BIOINFORMATICS

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

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

Large-scale prediction of drug-target relationships

(2008) Michael Kuhn et al.   FEBS LETTERS

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology