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iProClass: an integrated database of protein family, function and structure information
Hongzhan Huang1, Winona C Barker, Yongxing Chen
1Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA.
Nucleic Acids Research
|January 10, 2003
Summary
The iProClass database integrates protein data, offering comprehensive family, structural, and functional classifications. This resource aids in understanding protein evolution, structure, and function for genomic and proteomic research.
Area of Science:
- Proteomics
- Bioinformatics
- Structural Biology
Background:
- Protein databases are essential for organizing and accessing vast amounts of biological information.
- Integrating diverse protein data, including sequences, structures, and functions, is crucial for comprehensive analysis.
- Existing resources may lack integrated views of protein family relationships and functional annotations.
Purpose of the Study:
- To present the iProClass database as a comprehensive resource for protein information.
- To highlight iProClass's capabilities in data integration and providing value-added descriptions of proteins.
- To facilitate the exploration of protein relationships for evolutionary and functional studies.
Main Methods:
- The iProClass database integrates data from PIR-PSD, SWISS-PROT, and TrEMBL.
- It organizes proteins into superfamilies, families, domains, and motifs, with FASTA similarity clusters.
- Rich links to over 50 external databases enhance data accessibility and cross-referencing.
Main Results:
- The current version contains approximately 830,000 non-redundant proteins.
- It includes over 36,000 superfamilies, 145,000 families, 4,000 domains, and 1,300 motifs.
- Summary reports offer extensive annotation, membership statistics, and graphical domain/motif displays.
Conclusions:
- iProClass provides a robust framework for protein data integration and analysis.
- Its open architecture ensures interoperability and scalability for future development.
- The database is freely accessible and supports fundamental research in protein evolution, structure, and function.