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

By Alexis Lamiable, Pierre Thévenet, Julien Rey, Marek Vavrusa, Philippe Derreumaux, Pierre Tufféry. Nucleic Acids Res., 2016

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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 3.3Å 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.

Subfields: Microbiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e3cd28e118c7ccb5356738153b9b180e00fd0238