The Human Protein Reference Database (HPRD)
The Human Protein Reference Database (HPRD) curates and integrates genomic and proteomic information on human proteins, providing manually annotated data on protein-protein interactions, post-translational modifications, enzyme-substrate relationships, disease associations, tissue expression, and subcellular localization for research use.
Key Features:
- Protein-protein interactions: Manually annotated interactions between human proteins extracted from the literature.
- Post-translational modifications: Curated information on experimentally reported post-translational modifications.
- Enzyme-substrate relationships: Catalogued enzyme-substrate pairs drawn from published studies.
- Disease associations: Annotated links between proteins and disease states reported in the literature.
- Tissue expression: Curated evidence of tissue-specific protein expression.
- Subcellular localization: Annotated subcellular localization information for human proteins.
- Nonredundant protein set: Contains a nonredundant collection of approximately 2,750 human proteins.
- Literature curation: Annotations derived from manual extraction from over 300,000 published articles.
- Integrated sequence/structure/function/network links: Cross-references protein sequence, structure, function, and interaction networks within the database.
Scientific Applications:
- Biomedical research: Supporting studies of protein function, interactions, and alterations in health and disease contexts.
- Network and pathway analysis: Enabling construction and interpretation of protein interaction and functional networks.
- Disease mechanism discovery: Facilitating identification of proteins implicated in disease and their molecular relationships.
- Proteomics and genomics integration: Serving as a reference to integrate diverse genomic and proteomic data sources.
Methodology:
Implements a web-based platform that leverages open-source technologies and integrates manually curated annotations from the scientific literature.
Topics
Collections
Details
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- Python
- Added:
- 3/30/2017
- Last Updated:
- 11/25/2024
Operations
Data Inputs & Outputs
Publications
Peri S. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Research. 2004;32(90001):497D-501. doi:10.1093/nar/gkh070. PMID:14681466. PMCID:PMC308804.
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi T, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar H, Rashmi B, Ramya M, Zhao Z, Chandrika K, Padma N, Harsha H, Yatish A, Kavitha M, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans. Genome Research. 2003;13(10):2363-2371. doi:10.1101/gr.1680803. PMID:14525934. PMCID:PMC403728.