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Statistical prediction of protein–chemical interactions based on chemical structure and mass spectrometry data

Statistical prediction of protein–chemical interactions based on chemical structure and mass... Motivation: Prediction of interactions between proteins and chemical compounds is of great benefit in drug discovery processes. In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability.Results: We describe a novel method for predicting protein–chemical interaction using SVM. We utilize very general protein data, i.e. amino acid sequences, and combine these with chemical structures and mass spectrometry (MS) data. MS data can be of great use in finding new chemical compounds in the future. We assessed the validity of our method in the dataset of the binding of existing drugs and found that more than 80% accuracy could be obtained. Furthermore, we conducted comprehensive target protein predictions for MDMA, and validated the biological significance of our method by successfully finding proteins relevant to its known functions.Availability: Available on request from the authors.Contact: [email protected] information: Appendix–technical details of method, Supplementary Table 1–7 and Supplementary Figure 1. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

Statistical prediction of protein–chemical interactions based on chemical structure and mass spectrometry data

Nagamine, Nobuyoshi; Sakakibara, Yasubumi
Bioinformatics , Volume 23 (15): 9 – May 17, 2007
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References (35)

Publisher
Oxford University Press
Copyright
© 2007 The Author(s)
eISSN
1367-4811
DOI
10.1093/bioinformatics/btm266
pmid
17510168
Publisher site
See Article on Publisher Site

Abstract

Motivation: Prediction of interactions between proteins and chemical compounds is of great benefit in drug discovery processes. In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability.Results: We describe a novel method for predicting protein–chemical interaction using SVM. We utilize very general protein data, i.e. amino acid sequences, and combine these with chemical structures and mass spectrometry (MS) data. MS data can be of great use in finding new chemical compounds in the future. We assessed the validity of our method in the dataset of the binding of existing drugs and found that more than 80% accuracy could be obtained. Furthermore, we conducted comprehensive target protein predictions for MDMA, and validated the biological significance of our method by successfully finding proteins relevant to its known functions.Availability: Available on request from the authors.Contact: [email protected] information: Appendix–technical details of method, Supplementary Table 1–7 and Supplementary Figure 1.

Journal

Bioinformatics – Oxford University Press

Published: May 17, 2007

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