PepBank -- a database of peptides based on sequence text mining and public peptide data sources

What you can do:
A searchable archive for peptide sequences and associated biological data.
  • Contains a total of 19,792 individual peptide entries.
  • The database has a web-based user interface with a simple, Google-like search function, advanced text search, and BLAST and Smith-Waterman search capabilities.
  • The major source of peptide sequence data comes from text mining of MEDLINE abstracts.
  • Another component of the database is the peptide sequence data from public sources (ASPD and UniProt).
  • An additional, smaller part of the database is manually curated from sets of full text articles and text mining results.
  • The database has biological and medical applications, for example, to predict the binding partners of biologically interesting peptides, to develop peptide based therapeutic or diagnostic agents, or to predict molecular targets or binding specificities of peptides resulting from phage display selection.
  • The text mining source code (Peptide::Pubmed) is freely available on CPAN (
  • Amino Acid Sequence
  • Protein database
  • Molecular Sequence Data
  • Peptides
  • Sequence Analysis
  • Ligand discovery
  • binding partners
  • molecular target prediction
  • peptide based therapeutic agents
  • peptide based diagnostic agents
This record last updated: 04-09-2008
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