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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
DB-PABP: a database of polyanion-binding proteins.
Jianwen Fang1, Yinghua Dong, Nazila Salamat-Miller
1Bioinformatics Core Facility, Information and Telecommunication Technology Center, University of Kansas, Lawrence, KS 66047, USA.
Nucleic Acids Research
|October 6, 2007
Summary
This study introduces DB-PABP, a comprehensive database for polyanion-binding proteins (PABPs) and their interactions. It aids research into biological processes and neurodegenerative diseases by organizing scattered literature.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Polyanion-protein interactions are crucial for cellular functions like organization and transport.
- Many proteins implicated in neurodegenerative diseases bind polyanions, highlighting the importance of these interactions.
- Existing literature on polyanion-binding proteins (PABPs) is fragmented, necessitating a centralized resource.
Purpose of the Study:
- To develop a comprehensive, manually curated, and searchable database of experimentally characterized PABPs.
- To facilitate a deeper understanding of PA/PABP interactions for biological research and disease insights.
- To provide a freely accessible online resource for the scientific community.
Main Methods:
- Implementation of a MySQL relational database for storing PABP data.
- Development of an interactive web interface using Java Server Pages (JSP).
- Inclusion of advanced search functionalities (protein/polyanion names, species, methods) and utilities (commonality matrix, author search).
Main Results:
- The DB-PABP database is now available online, offering a centralized repository of PABP information.
- The database allows for custom searches and provides utilities to explore PABP interaction data.
- It serves as a valuable tool for researchers studying biological systems and neurodegenerative diseases.
Conclusions:
- DB-PABP provides a much-needed, organized resource for the study of polyanion-binding proteins.
- This database can accelerate research into fundamental biological processes and the molecular mechanisms of neurodegenerative diseases.
- The creators encourage user feedback and data submission to ensure the database remains current and comprehensive.
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