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Medicinal Chemistry
ISSN (Print): 1573-4064
ISSN (Online): 1875-6638
VOLUME: 6
ISSUE: 6
DOI: 10.2174/157340610793563983      Price:  $58









Using Compound Similarity and Functional Domain Composition for Prediction of Drug-Target Interaction Networks

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Author(s): Lei Chen, Zhi-Song He, Tao Huang and Yu-Dong Cai
Pages 388-395 (8)
Abstract:
Study of interactions between drugs and target proteins is an essential step in genomic drug discovery. It is very hard to determine the compound-protein interactions or drug-target interactions by experiment alone. As supplementary, effective prediction model using machine learning or data mining methods can provide much help. In this study, a prediction method based on Nearest Neighbor Algorithm and a novel metric, which was obtained by combining compound similarity and functional domain composition, was proposed. The target proteins were divided into the following groups: enzymes, ion channels, G protein-coupled receptors, and nuclear receptors. As a result, four predictors with the optimal parameters were established. The overall prediction accuracies, evaluated by jackknife cross-validation test, for four groups of target proteins are 90.23%, 94.74%, 97.80%, and 97.51%, respectively, indicating that compound similarity and functional domain composition are very effective to predict drug-target interaction networks.
Keywords:
Compound similarity, drug-target interaction network, functional domain composition, jackknife cross-validation test, Matthew's correlation coefficient, nearest neighbor algorithm, SMILES, MACC, SBASE-A
Affiliation:
Institute of Systems Biology, Shanghai University, People's Republic of China.