PEP-FOLD3: fasterde novostructure prediction for linear peptides in solution and in complex

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ID: 300902
2016
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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 3.3Å 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.
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Authors Alexis Lamiable, P. Thévenet, Julien Rey, Marek Vavruša, Philippe Derreumaux, Pierre Tufféry
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Journal Nucleic Acids Research
Year 2016
DOI
10.1093/nar/gkw329
URL
https://academic.oup.com/nar/article-pdf/44/W1/W449/18787567/gkw329.pdf
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