May 7, 2015

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

Nucleic Acids Research
Mateusz KurcinskiSebastian Kmiecik

Abstract

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is fr...Continue Reading

  • References23
  • Citations66

References

Mentioned in this Paper

Establishment and Maintenance of Localization
Fluctuation
Molecular Docking Simulation
Docking -molecular Interaction
Ligand Binding Domain
Pharmacologic Substance
Aminoacid Sequence of Protein
Binding (Molecular Function)
Protein Domain
Molecular Docking Analysis

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