biostudies-literatureUnknown9(5)Li HStructural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a foldinPloS onee94769https://www.ebi.ac.uk/biostudies/studies/S-EPMC4011740biostudies-literaturePaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.PMC4011740Li HLu LXia XQuan LChen RLu QfalsePaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a foldin2014-01-01T00:00:00Z20142026-05-03T22:34:02.236Z2019-03-26T23:24:39ZS-EPMC40117402480149610.1371/journal.pone.0094769