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Computational Overview of GPCR Gene Universe to Support Reverse Chemical Genomics Study

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Reverse Chemical Genetics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 577))

Summary

In order to support high-throughput screening for ligands of G-protein coupled receptors (GPCRs) by using bioinformatics technology, we introduce a database (SEVENS) with genome-scale annotation and software (GRIFFIN) that can simulate GPCR function. SEVENS (http://sevens.cbrc.jp/) is an integrated database that includes GPCR genes that are identified with high accuracy (99.4% sensitivity and 96.6% specificity) from various types of genomes, by a pipeline that integrates such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix (TMH) predictor. SEVENS provides the user a genome-scale overview of the “GPCR universe” with detailed information of chromosomal mapping, phylogenetic tree, protein sequence and structure, and experimental evidence, all of which are accessible via a user-friendly interface. GRIFFIN (http://griffin.cbrc.jp/) can predict GPCR and G-protein coupling selectivity induced by ligand binding with high sensitivity and specificity (more than 87% on average), based on the support vector machine (SVM) and hidden Markov Model (HMM). SEVENS and GRIFFIN are expected to contribute to revealing the function of orphan and unknown GPCRs.

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Acknowledgment

This work was supported by a Grant-in-Aid for special projects in genome science from the Ministry of Education Culture, Sports, Science, and Technology of Japan. We would like to thank Dr. Wataru Fujibuchi, Dr. Takatsugu Hirokawa, Mr. Yukimitsu Yabuki, and Mr. Tatsuya Nishizawa for helpful discussion in the course of SEVENS and GRIFFIN development.

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Authors and Affiliations

  1. Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

    Makiko Suwa & Yukiteru Ono

Authors
  1. Makiko Suwa
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  2. Yukiteru Ono
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Editors and Affiliations

  1. Iwai Orthopaedic Medical Hospital, Minamikoiwa 8-17-5, Tokyo, 133-0055, Japan

    Hisashi Koga

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Suwa, M., Ono, Y. (2009). Computational Overview of GPCR Gene Universe to Support Reverse Chemical Genomics Study. In: Koga, H. (eds) Reverse Chemical Genetics. Methods in Molecular Biology™, vol 577. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-232-2_4

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  • DOI: https://doi.org/10.1007/978-1-60761-232-2_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-231-5

  • Online ISBN: 978-1-60761-232-2

  • eBook Packages: Springer Protocols

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