Komiyama Y, Banno M, Ueki K, Saad G, Shimizu K. Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.
ACTA ACUST UNITED AC 2015;
32:901-7. [PMID:
26545824 PMCID:
PMC4803387 DOI:
10.1093/bioinformatics/btv593]
[Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022]
Abstract
MOTIVATION
Predictive tools that model protein-ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein-ligand binding predictive tools would be useful.
RESULTS
We developed a system for automatically generating protein-ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5-1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands.
AVAILABILITY AND IMPLEMENTATION
The source code and web application are freely available for download at http://utprot.net They are implemented in Python and supported on Linux.
CONTACT
shimizu@bi.a.u-tokyo.ac.jp
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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