AMPer: a database and an automated discovery tool for antimicrobial peptides

Bioinformatics. 2007 May 1;23(9):1148-55. doi: 10.1093/bioinformatics/btm068. Epub 2007 Mar 6.


Motivation: Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may offer one possible solution. In the current study, we utilized publicly available data on AMPs to construct hidden Markov models (HMMs) that enable recognition of individual classes of antimicrobials peptides (such as defensins, cathelicidins, cecropins, etc.) with up to 99% accuracy and can be used for discovering novel AMP candidates.

Results: HMM models for both mature peptides and propeptides were constructed. A total of 146 models for mature peptides and 40 for propeptides have been developed for individual AMP classes. These were created by clustering and analyzing AMP sequences available in the public sources and by consequent iterative scanning of the Swiss-Prot database for previously unknown gene-coded AMPs. As a result, an additional 229 additional AMPs have been identified from Swiss-Prot, and all but 34 could be associated with known antimicrobial activities according to the literature. The final set of 1045 mature peptides and 253 propeptides have been organized into the open-source AMPer database.

Availability: The developed HMM-based tools and AMP sequences can be accessed through the AMPer resource at

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Antimicrobial Cationic Peptides / chemistry*
  • Artificial Intelligence*
  • Database Management Systems
  • Databases, Protein*
  • Information Storage and Retrieval / methods*
  • Molecular Sequence Data
  • Sequence Analysis, Protein / methods*
  • Software*
  • User-Computer Interface*


  • Antimicrobial Cationic Peptides