Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets

Adam Krejci, Ted R. Hupp, Matej Lexa, Borivoj Vojtesek, Petr Muller

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Proteins often recognize their interaction partners on the basis of short linear motifs located in disordered regions on proteins' surface. Experimental techniques that study such motifs use short peptides to mimic the structural properties of interacting proteins. Continued development of these methods allows for large-scale screening, resulting in vast amounts of peptide sequences, potentially containing information on multiple protein-protein interactions. Processing of such datasets is a complex but essential task for large-scale studies investigating protein-protein interactions.

Results: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters. The method was applied on a previously published smaller dataset containing distinct classes of ligands for SH3 domains, as well as on a new, an order of magnitude larger dataset containing epitopes for several monoclonal antibodies. The software successfully identified clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Another test indicates that processing of even much larger datasets is computationally feasible.

Original languageEnglish
Pages (from-to)9-16
Number of pages8
JournalBioinformatics
Volume32
Issue number1
Early online date5 Sep 2015
DOIs
Publication statusE-pub ahead of print - 5 Sep 2015

Keywords

  • PREDICTION
  • LIBRARIES
  • GALAXY
  • GENERATION
  • EPITOPES
  • PLATFORM

Cite this