Prediction of compound-protein interactions with machine learning methods

Yoshihiro Yamanishi, Hisashi Kashima

Research output: Chapter in Book/Report/Conference proceedingChapter


In silico prediction of compound-protein interactions from heterogeneous biological data is critical in the process of drug development. In this chapter the authors review several supervised machine learning methods to predict unknown compound-protein interactions from chemical structure and genomic sequence information simultaneously. The authors review several kernel-based algorithms from two different viewpoints: binary classification and dimension reduction. In the results, they demonstrate the usefulness of the methods on the prediction of drug-target interactions and ligand-protein interactions from chemical structure data and genomic sequence data.

Original languageEnglish
Title of host publicationChemoinformatics and Advanced Machine Learning Perspectives
Subtitle of host publicationComplex Computational Methods and Collaborative Techniques
PublisherIGI Global
Number of pages14
ISBN (Print)9781615209118
Publication statusPublished - 2010
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Agricultural and Biological Sciences


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