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09:15
Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
Published on: January 10, 2018
coliSNP database server mapping nsSNPs on protein structures.
Hidetoshi Kono1, Tomo Yuasa, Shinya Nishiue
1Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto 619-0215, PRESTO, Japan. kono.hidetoshi@jaea.go.jp
Nucleic Acids Research
|October 9, 2007
Summary
We created coliSNP, a database mapping protein non-synonymous single nucleotide polymorphisms (nsSNPs) onto 3D structures. This tool helps assess how nsSNPs impact protein function and stability using integrated SNP and structural data.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- Single nucleotide polymorphisms (SNPs) can alter protein function.
- Understanding the structural impact of non-synonymous SNPs (nsSNPs) is crucial for disease research.
- Existing databases often lack integrated protein structure information for nsSNPs.
Purpose of the Study:
- To develop a comprehensive database server, coliSNP, for mapping nsSNPs onto protein 3D structures.
- To provide a tool for assessing the potential functional and stability impacts of nsSNPs.
- To integrate data from dbSNP and the Protein Data Bank (PDB) for nsSNP analysis.
Main Methods:
- Automated weekly downloads of SNP data from dbSNP and protein structure data from PDB.
- Tabulation of correspondence between SNP and protein structure data in the coliSNP database.
- Development of a web server allowing users to query nsSNP information via amino acid sequence, protein name, or PDB ID.
Main Results:
- The coliSNP server provides detailed information on nsSNPs, including amino acid mutations, solvent accessibility, secondary structure, and flanking residues.
- Users can visualize the position of nsSNPs within both the amino acid sequence and the 3D protein structure.
- The database facilitates the evaluation of nsSNP effects on protein function and stability.
Conclusions:
- coliSNP is a unique web-based resource for analyzing nsSNPs in the context of protein structure.
- The automated compilation of SNP and protein data offers a concise and valuable tool for researchers.
- This resource aids in predicting the functional significance of genetic variations at the protein level.
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