PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex

TitlePEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex
Publication TypeJournal Article
Year of Publication2016
AuthorsLamiable A, Thevenet P, Rey J, Vavrusa M, Derreumaux P, Tuffery P
JournalNucleic Acids Res.
Volume44
PaginationW449-W454
ISSN0305-1048
Abstract

Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3 angstrom from the experimental conformation and return a native-like pose in the first 10 clusters for 52% of the targets. PEP-FOLD3 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.

DOI10.1093/nar/gkw329
Citation Key2016|1733