Similarity-based machine learning methods for predicting drug–target interactions: a brief review
Open Access
- 10 August 2013
- journal article
- review article
- Published by Oxford University Press (OUP) in Briefings in Bioinformatics
- Vol. 15 (5), 734-747
- https://doi.org/10.1093/bib/bbt056
Abstract
Computationally predicting drug–target interactions is useful to select possible drug (or target) candidates for further biochemical verification. We focus on machine learning-based approaches, particularly similarity-based methods that use drug and target similarities, which show relationships among drugs and those among targets, respectively. These two similarities represent two emerging concepts, the chemical space and the genomic space. Typically, the methods combine these two types of similarities to generate models for predicting new drug–target interactions. This process is also closely related to a lot of work in pharmacogenomics or chemical biology that attempt to understand the relationships between the chemical and genomic spaces. This background makes the similarity-based approaches attractive and promising. This article reviews the similarity-based machine learning methods for predicting drug–target interactions, which are state-of-the-art and have aroused great interest in bioinformatics. We describe each of these methods briefly, and empirically compare these methods under a uniform experimental setting to explore their advantages and limitations.Keywords
This publication has 64 references indexed in Scilit:
- Large-scale prediction and testing of drug activity on side-effect targetsNature, 2012
- Mining small-molecule screens to repurpose drugsBriefings in Bioinformatics, 2011
- Exploiting drug-disease relationships for computational drug repositioningBriefings in Bioinformatics, 2011
- Predicting drug side-effect profiles: a chemical fragment-based approachBMC Bioinformatics, 2011
- Identify drug repurposing candidates by mining the Protein Data BankBriefings in Bioinformatics, 2011
- Predicting promiscuityNature, 2009
- From genomics to chemical genomics: new developments in KEGGNucleic Acids Research, 2006
- Chemical space and biologyNature, 2004
- The druggable genomeNature Reviews Drug Discovery, 2002
- Chemical genetics: ligand-based discovery of gene functionNature Reviews Genetics, 2000