title: PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.
abstract: 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 folding peptide with a flexible receptor. This approach mimics the actual protein-peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein-peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Haiou
authors.initials: H
authors.lastname: Li
authors.affiliation: Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
authors.forename: Liyao
authors.initials: L
authors.lastname: Lu
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Lijun
authors.initials: L
authors.lastname: Quan
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China; Jiangsu Provincial Key Lab for Information Processing Technologies, Suzhou, Jiangsu, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Xia
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou, Jiangsu, China; Jiangsu Provincial Key Lab for Information Processing Technologies, Suzhou, Jiangsu, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Lü
mesh_terms: D000595:Amino Acid Sequence; D062105:Molecular Docking Simulation / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D018000:Receptors, Peptide / Q000737:chemistry* / Q000378:metabolism
chemical_list: D010455:Peptides; D018000:Receptors, Peptide