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Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54. doi: 10.1093/nar/gkw329. Epub 2016 Apr 29.

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

Author information

1
Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France.
2
Institut de Biologie Physico Chimique, Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, CNRS UPR 9080, 75005 Paris, France.
3
Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France pierre.tuffery@univ-paris-diderot.fr.

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.

PMID:
27131374
PMCID:
PMC4987898
DOI:
10.1093/nar/gkw329
[Indexed for MEDLINE]
Free PMC Article

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