Molecular evaluation using in silico protein interaction profiles.

Yoshiharu Hayashi; Katsuyoshi Sakaguchi; Mime Kobayashi; Masaki Kobayashi; Yo Kikuchi; Eiichiro Ichiishi

doi:10.1093/bioinformatics/btg189

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Molecular evaluation using in silico protein interaction profiles.

Yoshiharu Hayashi·Katsuyoshi Sakaguchi·Mime Kobayashi·Masaki Kobayashi·Yo Kikuchi·Eiichiro Ichiishi

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Abstract

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.

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Algorithms Binding Sites Computer Simulation Energy Transfer Macromolecular Substances Models, Chemical Models, Molecular Protein Array Analysis Protein Binding Protein Interaction Mapping Proteins Quantitative Structure-Activity Relationship Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't Validation Study

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Yoshiharu Hayashi, Katsuyoshi Sakaguchi, Mime Kobayashi, Masaki Kobayashi, Yo Kikuchi, Eiichiro Ichiishi. 2003-08-12. Molecular evaluation using in silico protein interaction profiles.. https://doi.org/10.1093/bioinformatics%2Fbtg189

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