Computational overview of GPCR gene universe to support reverse chemical genomics study

Methods Mol Biol. 2009;577:41-54. doi: 10.1007/978-1-60761-232-2_4.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Artificial Intelligence
  • Computational Biology
  • Databases, Genetic*
  • Drug Design
  • Drug Evaluation, Preclinical / methods
  • Drug Evaluation, Preclinical / statistics & numerical data
  • Genomics / methods*
  • Genomics / statistics & numerical data
  • High-Throughput Screening Assays / statistics & numerical data
  • Humans
  • Ligands
  • Markov Chains
  • Proteomics / methods
  • Proteomics / statistics & numerical data
  • Receptors, G-Protein-Coupled / chemistry
  • Receptors, G-Protein-Coupled / genetics*
  • Receptors, G-Protein-Coupled / metabolism
  • Software

Substances

  • Ligands
  • Receptors, G-Protein-Coupled