ArticleBMC bioinformatics2007
PepBank--a database of peptides based on sequence text mining and public peptide data sources.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
66 citing papers in PubMed.
- Bioactive Peptides From theFood science & nutrition · 2026Review
- Review
- Harnessing Machine Learning Approaches for the Identification, Characterization, and Optimization of Novel Antimicrobial Peptides.Antibiotics (Basel, Switzerland) · 2025Review
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Overview and limitations of database in global traditional medicines: A narrative review.Acta pharmacologica Sinica · 2025Review
- Guide to Selection of Muscle-Homing Peptides After in Vivo Phage Display Biopanning.Methods in molecular biology (Clifton, N.J.) · 2025Article
- From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials.Journal of chemical information and modeling · 2024Article
- Identification of Potential Bioactive Peptides in Sheep Milk Kefir through Peptidomic Analysis at Different Fermentation Times.Foods (Basel, Switzerland) · 2023Article
- In Silico Prospecting for Novel Bioactive Peptides from Seafoods: A Case Study on Pacific Oyster (Molecules (Basel, Switzerland) · 2023Article
- Enzymatic synthesis of new antimicrobial peptides for food purposes.Frontiers in microbiology · 2023Article
- Peptide Utility (PU) search server: A new tool for peptide sequence search from multiple databases.Heliyon · 2022Article
- MPMABP: A CNN and Bi-LSTM-Based Method for Predicting Multi-Activities of Bioactive Peptides.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Antioxidant and Antimicrobial Peptides Derived from Food Proteins.Molecules (Basel, Switzerland) · 2022Review
- Computational identification and characterization of antigenic properties of Rv3899c of Mycobacterium tuberculosis and its interaction with human leukocyte antigen (HLA).Immunogenetics · 2021Article
- Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes.Molecules (Basel, Switzerland) · 2021Article
- Can the SARS-CoV-2 Spike Protein Bind Integrins Independent of the RGD Sequence?Frontiers in cellular and infection microbiology · 2021Article
- Biosynthesis of a Novel Antibacterial Dipeptide, Using Proteases From South American Native Fruits, Useful as a Food Preservative.Frontiers in nutrition · 2021Article
- Box Jellyfish (Cnidaria, Cubozoa) Extract Increases Neuron's Connection: A Possible Neuroprotector Effect.BioMed research international · 2021Article
- DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands.Database : the journal of biological databases and curation · 2020Article
- Marine Bioactive Peptides-An Overview of Generation, Structure and Application with a Focus on Food Sources.Marine drugs · 2020Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
backgroundPeptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated biological data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources. DESCRIPTION: We have constructed a new database (PepBank), which at the time of writing 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. We show the utility of the database in different examples of affinity ligand discovery.
conclusionWe have created and maintain a database of peptide sequences. 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 database is freely available on http://pepbank.mgh.harvard.edu/, and the text mining source code (Peptide::Pubmed) is freely available above as well as on CPAN (http://www.cpan.org/).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.