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PDZscape: a comprehensive PDZ-protein database.
Jitesh Doshi1, Raja Reddy Kuppili1,2, Siddharth Gurdasani1,3
1Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410210, India.
BMC Bioinformatics
|April 28, 2018
Summary
PDZscape is a new database detailing 58,648 PDZ-containing proteins and their interactions. It integrates multiple databases and includes disease-associated mutations, offering a comprehensive resource for cell signaling research.
Area of Science:
- Molecular Biology
- Bioinformatics
- Cellular Signaling
Background:
- PDZ-containing proteins are crucial for cell localization, membrane receptor clustering, and signal transduction.
- The existing PDZBase database is outdated and limited, containing only 339 proteins.
- A comprehensive, up-to-date resource for PDZ-containing proteins is needed.
Purpose of the Study:
- To develop PDZscape, a comprehensive database for PDZ-containing proteins and their interactomes.
- To integrate diverse biological databases for a unified view of PDZ protein information.
- To provide tools for querying and analyzing PDZ protein data, including mutations and diseases.
Main Methods:
- Development of a user-friendly web interface for PDZscape.
- Integration of data from NCBI, UniProtKB, Swiss-Prot, Pubmed, PDB, STRING, IntAct, KEGG, Pfam, and Protein Mutant Database.
- Manual curation of mutations and diseases associated with PDZ-containing proteins.
Main Results:
- PDZscape contains information on 58,648 PDZ-containing proteins and their known/putative binding partners.
- The database offers a user-friendly interface with a customized BLAST option (PDZ-Blast).
- Detailed information on the PDZ interactome, including mutations and associated diseases, is provided.
Conclusions:
- PDZscape is a comprehensive and freely available resource for studying PDZ-containing proteins.
- The database facilitates research on cell signaling pathways and related diseases.
- PDZscape enhances the understanding of PDZ protein functions and interactions.
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