MOESM1 of Efficient conformational ensemble generation of protein-bound peptides

Additional file 1. The average accuracies and standard deviations of MODPEP for the peptides of 3–30 amino acids on ten randomly splitted training/test sets

Additional file 1 of Association of dietary inflammatory index and the SARS-CoV-2 infection incidence, severity and mortality of COVID-19: a systematic review and dose-response meta-analysis

Supplementary Material

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

Given the importance of peptide-mediated protein interactions in cellular processes, protein–peptide docking has received increasing attention. Here, we have developed a <b>H</b>ierarchical flexible <b>Pep</b>tide <b>Dock</b>ing approach through fast generation and ensemble docking of peptide conformations, which is referred to as <b>HPepDock</b>. 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