Portal de Periódicos da CAPES

Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides

2018; American Chemical Society; Volume: 58; Issue: 6 Linguagem: Inglês

10.1021/acs.jcim.8b00142

1549-960X

Pei Zhou, Botong Li, Yumeng Yan, Bowen Jin, Libang Wang, Sheng‐You Huang,

Chemical Synthesis and Analysis

Given the importance of peptide-mediated protein interactions in cellular processes, protein–peptide docking has received increasing attention. Here, we have developed a Hierarchical flexible Peptide Docking approach through fast generation and ensemble docking of peptide conformations, which is referred to as HPepDock. Tested on the LEADS-PEP benchmark data set of 53 diverse complexes with peptides of 3–12 residues, HPepDock performed significantly better than the 11 docking protocols of five small-molecule docking programs (DOCK, AutoDock, AutoDock Vina, Surflex, and GOLD) in predicting near-native binding conformations. HPepDock was also evaluated on the 19 bound/unbound and 10 unbound/unbound protein–peptide complexes of the Glide SP-PEP benchmark and showed an overall better performance than Glide SP-PEP+MM-GBSA and FlexPepDock in both bound and unbound docking. HPepDock is computationally efficient, and the average running time for docking a peptide is ∼15 min with the range from about 1 min for short peptides to around 40 min for long peptides.