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Drug Discov Today. 2018 Aug;23(8):1530-1537. doi: 10.1016/j.drudis.2018.05.006. Epub 2018 May 4.

Protein-peptide docking: opportunities and challenges.

Author information

1
Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland; Faculty of Physics, University of Warsaw, Warsaw, Poland.
2
Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
3
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
4
Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
5
Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland. Electronic address: sekmi@chem.uw.edu.pl.

Abstract

Peptides have recently attracted much attention as promising drug candidates. Rational design of peptide-derived therapeutics usually requires structural characterization of the underlying protein-peptide interaction. Given that experimental characterization can be difficult, reliable computational tools are needed. In recent years, a variety of approaches have been developed for 'protein-peptide docking', that is, predicting the structure of the protein-peptide complex, starting from the protein structure and the peptide sequence, including variable degrees of information about the peptide binding site and/or conformation. In this review, we provide an overview of protein-peptide docking methods and outline their capabilities, limitations, and applications in structure-based drug design. Key challenges are also briefly discussed, such as modeling of large-scale conformational changes upon binding, scoring of predicted models, and optimal inclusion of varied types of experimental data and theoretical predictions into an integrative modeling process.

PMID:
29733895
DOI:
10.1016/j.drudis.2018.05.006
[Indexed for MEDLINE]
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