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GTOP: a database of protein structures predicted from genome sequences
Takeshi Kawabata1, Satoshi Fukuchi, Keiichi Homma
1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1-111 Yata, Mishima, Shizuoka 411-8540, Japan.
Nucleic Acids Research
|December 26, 2001
Summary
The Genomes TO Protein structures and functions (GTOP) database predicts 3D protein structures for over 120,000 sequences from 41 organisms. This resource aids in understanding protein function for uncharacterized sequences.
Area of Science:
- Genomics
- Structural Biology
- Bioinformatics
Background:
- Large-scale genome projects yield numerous uncharacterized protein sequences.
- Predicting protein 3D structures is crucial for inferring function.
- Existing methods require efficient tools for large-scale analysis.
Purpose of the Study:
- To develop and present the Genomes TO Protein structures and functions (GTOP) database.
- To provide protein fold predictions and functional insights for a vast number of protein sequences.
- To integrate various bioinformatic analyses for comprehensive protein characterization.
Main Methods:
- Utilized PSI-BLAST for high-sensitivity homology-based protein structure prediction.
- Incorporated additional analyses including homology and motif searches.
- Developed a graphical viewer for presenting results in a 'color-bar' format.
Main Results:
- Constructed the GTOP database with over 120,000 protein sequences from 41 organisms.
- Generated protein fold predictions and identified binding sites for ligands.
- Integrated 3D structure visualization using Chime plug-in and RasMol.
Conclusions:
- The GTOP database offers a valuable resource for exploring protein structures and functions.
- Facilitates the functional annotation of newly discovered proteins from genome projects.
- Provides a centralized platform for integrated bioinformatic analysis of protein sequences.