title: PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
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.
authors.affiliation: Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Lamiable
authors.affiliation: Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Thévenet
authors.affiliation: Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Rey
authors.affiliation: Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France.
authors.forename: Marek
authors.initials: M
authors.lastname: Vavrusa
authors.affiliation: Institut de Biologie Physico Chimique, Laboratoire de Biochimie Théorique, Université Paris Diderot, Sorbonne Paris Cité, CNRS UPR 9080, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.affiliation: 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.
authors.forename: Pierre
authors.initials: P
authors.lastname: Tufféry
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D019985:Benchmarking; D020407:Internet; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012996:Solutions
chemical_list: D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D012996:Solutions