Title: LigSeeSVM: Ligand-based virtual Screening using Support Vector Machines and data fusion

Authors: Yen-Fu Chen, Kai-Cheng Hsu, Po-Tsun Lin, D. Frank Hsu, Bruce S. Kristal, Jinn-Moon Yang

Addresses: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan. ' Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan. ' Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan. ' Department of Computer and Information Science, Fordham University, New York, NY 10023, USA. ' Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA. ' Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30050, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30050, Taiwan; Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan

Abstract: Ligand-based in silico drug screening is useful for lead discovery, in particular for those targets without structures. Here, we have developed LigSeeSVM, a ligand-based screening tool using data fusion and Support Vector Machines (SVMs). We used Atom Pair (AP) structure descriptors and Physicochemical (PC) descriptors of compounds to generate SVM-AP and SVM-PC models. Sequentially, the two models were combined using rank-based data fusion to create LigSeeSVM model. LigSeeSVM was evaluated on five data sets. Experimental results show that the performance of LigSeeSVM is better than other ligand-based virtual screening approaches. We believe that LigSeeSVM is useful for lead compounds.

Keywords: ligand-based virtual screening; support vector machines; SVM; data fusion; rank combination; thymidine kinase substrates; oestrogen receptor; in silico drug screening; lead compounds.

DOI: 10.1504/IJCBDD.2011.041415

International Journal of Computational Biology and Drug Design, 2011 Vol.4 No.3, pp.274 - 289

Available online: 21 Jul 2011

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