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Bioinformatics Vol. 19 no. 12 2003
Pages 1514-1523
© 2003 Oxford University Press

Molecular evaluation using in silico protein interaction profiles

Yoshiharu Hayashi 1,2,3,*, Katsuyoshi Sakaguchi 1,3, Mime Kobayashi 4, Masaki Kobayashi 1, Yo Kikuchi 2 and Eiichiro Ichiishi 3,{dagger}

1 Division of Bioinformatics, KLIMERS (K-laboratories for Intelligent Medical Remote Services, Enkaku Iryou-laboratories) Co., Ltd., 2266-22 Anagahora, Shimoshidami, Moriyama-ku, Nagoya 463-0003, Japan
2 Department of Ecological Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi 441-8680, Japan
3 Functional Genomics and Proteomics Research Laboratory, First Department of Medicine, Kyoto Prefectural University of Medicine, 465 Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566 Japan
4 Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA

Received on October 4, 2002 ; revised on January 6, 2003 ; accepted on February 27, 2003

Motivation: To find a correlation between the activities and structures of molecules is one of the most important subjects for molecular evaluation study. Traditional quantitative structure-activity relationship (QSAR) methodologies represent those attempts using physicochemical descriptors. Creating a new molecular description factor based on the results of a computational docking study will add new dimensions to molecular evaluation.

Results: We propose a new molecular description factor analysis system called the Comparative Molecular Interaction Profile Analysis (CoMIPA) system in which the AutoDock program is used for docking evaluation of small molecule compound–protein complexes. Interaction energies are calculated, and the data sets obtained are called interaction profiles (IPFs). Using the IPF as a scoring indicator, the system could be a powerful tool to cluster the interacting properties between small molecules and bio macromolecules such as ligand–receptor bindings. Further development of the system will enable us to predict the adverse effects of a drug candidate.

Contact: yhayashi{at}enkaku.co.jp

* To whom correspondence should be addressed.

{dagger} Presend address: New Industry Creation Hatchery Center, Tohoku University, 10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.


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