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

Lamiable, Alexis ; Thevenet, Pierre ; Rey, Julien ; Vavrusa, Marek ; Derreumaux, Philippe ; Tufféry, Pierre

Nucleic acids research, 2016-07, Vol.44 (W1), p.W449-W454 [Periódico revisado por pares]

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Título:
PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex
Autor: Lamiable, Alexis ; Thevenet, Pierre ; Rey, Julien ; Vavrusa, Marek ; Derreumaux, Philippe ; Tufféry, Pierre
Assuntos: Biochemistry, Molecular Biology ; Biophysics ; Life Sciences
É parte de: Nucleic acids research, 2016-07, Vol.44 (W1), p.W449-W454
Notas: PMCID: PMC4987898
Descrição: 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 bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.
Editor: Oxford University Press
Idioma: Inglês

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