hprd

is an Aggregator.

The Human Protein Reference Database (HPRD) was a comprehensive, manually curated collection of information on human proteins, including protein-protein interactions, post-translational modifications (PTMs), enzyme-substrate relationships, subcellular localization, tissue expression, and disease associations. Developed through collaboration between the Institute of Bioinformatics in Bangalore, India and Johns Hopkins University in Baltimore, USA, HPRD contained over 20,000 protein entries with more than 36,500 unique protein-protein interactions and 18,000 PTMs before being discontinued. The database served as a major resource for the human proteome from 2003 to approximately 2010.

Domains

biomedical, proteomics, biological systems, systems biology

License

CC BY 3.0

Homepage

hprd

Repository

Unknown

Infores ID

Unknown

FAIRsharing ID

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Product Summary

Products

From this Resource
ID Name URL Category Format Description
hprd.ppi.data ⚠ HPRD Protein-Protein Interactions www.hprd.org Product psi_mi_mitab HPRD protein-protein interaction data...
hprd.xml.download ⚠ HPRD XML Data Download www.hprd.org DocumentationProduct ❔ HPRD data in XML format for programma...
hprd.tsv.download ⚠ HPRD Tab-Delimited Data Download www.hprd.org DocumentationProduct ❔ HPRD data in tab-delimited format for...
hprd.phosphomotif.finder ⚠ HPRD PhosphoMotif Finder www.hprd.org GraphicalInterface http PhosphoMotif Finder tool for identify...
hprd.genprot.viewer ⚠ GenProt Viewer www.genprot.org GraphicalInterface http GenProt Viewer for integrated genomic...
From other Resources
ID Name URL Category Format Description
irefindex.database iRefIndex Database ❔ Product psi_mi_mitab Historical consolidated protein inter...
string.protein.links STRING Protein Links protein.links.v12.0.txt.gz (128.7 GB) GraphProduct txt protein network data (full network, s...
string.protein.links.detailed STRING Protein Links Detailed protein.links.detailed.v12.0.txt.gz (189.6 GB) GraphProduct txt protein network data (full network, i...
string.protein.links.full STRING Protein Links Full protein.links.full.v12.0.txt.gz (199.6 GB) GraphProduct txt protein network data (full network, i...
string.protein.physical.links STRING Protein Physical Links protein.physical.links.v12.0.txt.gz (11.1 GB) GraphProduct txt protein network data (physical subnet...
string.protein.physical.links.detailed STRING Protein Physical Links Detailed protein.physical.links.detailed.v12.0.txt.gz (13.8 GB) GraphProduct txt protein network data (physical subnet...
string.protein.physical.links.full STRING Protein Physical Links Full protein.physical.links.full.v12.0.txt.gz (14.5 GB) GraphProduct txt protein network data (physical subnet...
string.cog.links STRING COG Links COG.links.v12.0.txt.gz (176.8 MB) GraphProduct txt association scores between orthologou...
string.cog.links.detailed STRING COG Links Detailed COG.links.detailed.v12.0.txt.gz (238.7 MB) GraphProduct txt association scores (incl. subscores p...
string.database STRING Database Network Schema network_schema.v12.0.sql.gz (262.2 GB) GraphProduct ❔ full database, part II: the networks ...

Details

HPRD - Human Protein Reference Database

Note: HPRD is no longer actively maintained. The website at www.hprd.org is currently inaccessible. HPRD data has been archived and incorporated into other protein interaction databases such as iRefIndex, IntAct, BioGRID, and STRING.

Overview

The Human Protein Reference Database (HPRD) was a pioneering resource in proteomics that provided comprehensive, manually curated information about human proteins. Developed through an international collaboration between the Institute of Bioinformatics in Bangalore, India and the Pandey Laboratory at Johns Hopkins University in Baltimore, USA, HPRD served as a major resource for understanding the human proteome and protein networks from 2003 to approximately 2010.

Key Statistics (Final Release)

  • 20,097 protein entries including 1,587 isoforms
  • 36,500+ unique protein-protein interactions (one of the largest manually curated collections at the time)
  • 18,000+ post-translational modifications across 26 different types
  • 3,343 enzyme-substrate relationships
  • 478 protein domains and motifs

Data Types Annotated

  1. Protein-Protein Interactions (PPIs)
    • Over 36,500 unique interactions
    • Categorized by experimental method:
      • In vivo experiments (19,175 interactions)
      • In vitro experiments (11,114 interactions)
      • Yeast two-hybrid (1,813 interactions)
    • Links to primary literature sources
  2. Post-Translational Modifications (PTMs)
    • 18,000+ manually curated PTMs
    • 26 different types of modifications
    • Major categories:
      • Phosphorylation (63% of PTM data, 5,011 events)
      • Glycosylation (1,132 events)
      • Proteolytic cleavage
      • Disulfide bridges
      • Others (acetylation, methylation, ubiquitination, etc.)
  3. Protein Features
    • Domain architecture
    • Protein motifs
    • Subcellular localization (including 489 nucleolar proteins and 270 secreted proteins)
    • Tissue expression patterns
    • Enzyme-substrate relationships
  4. Disease Associations
    • Links to OMIM (Online Mendelian Inheritance in Man)
    • Disease-related protein annotations

Special Features

PhosphoMotif Finder: A tool for identifying known kinase/phosphatase substrate and binding motifs based on literature-curated data. Unlike prediction tools, it reported the presence of experimentally validated motifs in query sequences.

GenProt Viewer: An integrated browser (www.genprot.org) that provided:

  • Genomic, transcriptomic, and proteomic views of the human genome
  • SNP mapping and annotations
  • Transcript information from RefSeq
  • Integration with Haploview for population haplotype patterns
  • Peptide sequence data from PeptideAtlas and PRIDE repositories

Pathway Integration: Curated signaling pathways visualized through GenMAPP (Gene Microarray Pathway Profiler), showing:

  • Protein-protein interactions in pathway context
  • Post-translational modifications
  • Protein shuttling between subcellular compartments
  • Enzymatic activity regulation
  • mRNA regulation

Data Formats

HPRD data was available in multiple formats:

  • PSI-MI format: Protein-protein interaction data in PSI-MI (Proteomics Standards Initiative - Molecular Interactions) level 2.5 format
  • XML format: Comprehensive database exports
  • Tab-delimited format: Simple text-based data files
  • Web interface: Interactive browsing and search capabilities

Integration and Legacy

HPRD was integrated with:

  • Human Proteinpedia: A community portal for sharing human protein data
  • RefSeq: NCBI reference sequences
  • Swiss-Prot: UniProt protein knowledge base
  • OMIM: Disease and gene associations
  • Entrez Gene: NCBI gene database

HPRD data has been archived and incorporated into several active databases:

  • iRefIndex: Historical consolidated protein interaction index
  • IntAct: Molecular interaction database
  • BioGRID: Biological General Repository for Interaction Datasets
  • STRING: Protein-protein interaction networks

Search Capabilities

HPRD supported multiple query options:

  • Gene symbols
  • RefSeq accession numbers
  • OMIM IDs
  • Swiss-Prot IDs
  • HPRD IDs
  • Entrez Gene IDs
  • BLAST search for sequence-based queries
  • Multiple parameter searches

Curation Process

All protein annotations in HPRD were:

  • Manually curated by expert biologists
  • Literature-derived from published scientific papers
  • Evidence-based with experimental support
  • Linked to primary sources with PubMed citations

Impact on Proteomics

HPRD made significant contributions to:

  • Systems biology approaches in human proteomics
  • Understanding of human protein interaction networks
  • Development of protein interaction databases
  • Standardization of protein interaction data formats (PSI-MI)
  • Integration of genomic, transcriptomic, and proteomic data

License

HPRD data was available for:

  • Academic use: Freely accessible and usable
  • Commercial use: Required a license

Human Proteinpedia content was freely available for anyone to download and use.

Current Status

HPRD is no longer actively maintained. The primary website (www.hprd.org) and associated GenProt Viewer (www.genprot.org) are currently inaccessible. However, the valuable data generated by HPRD has been preserved:

  • iRefIndex maintains HPRD interaction data in their historical consolidated index
  • IntAct, BioGRID, and STRING have incorporated HPRD interactions
  • Archive.org may have snapshots of the original website
  • Publications describing HPRD remain available and continue to be cited

For current protein-protein interaction data, users are encouraged to consult:

  • IntAct (www.ebi.ac.uk/intact/)
  • BioGRID (thebiogrid.org)
  • STRING (string-db.org)
  • HuRI - Human Reference Interactome (www.interactome-atlas.org)

Historical Significance

HPRD represented a landmark effort in manual curation of human protein data and set standards for:

  • Quality of manually curated protein interaction data
  • Integration of multiple data types (interactions, PTMs, localization, expression)
  • Community engagement through feedback mechanisms
  • Open data sharing in proteomics research

The database’s approach to systematic annotation and its emphasis on literature-derived evidence influenced the development of subsequent protein databases and resources in the proteomics field.

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Created: October 30, 2025 | Last modified: October 31, 2025