title: A case study of scoring and rescoring in peptide docking.
abstract: Previously, we examined the application of a molecular dynamics-based simulated annealing cycling protocol to docking peptides to proteins using two implicit-solvent models: a distance-dependent dielectric model (ε(r) = 4r) and a version of the Generalized Born model termed GBMV. We found that rescoring structures obtained from one implicit-solvent model with the other could improve the identification of the correct docking pose. Here, we guide interested readers on how to perform a similar study, using the docking between a hexapeptide and the protein phosphatase YopH inYersinia pestis as an example.
authors.affiliation: Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA.
authors.forename: Zunnan
authors.initials: Z
authors.lastname: Huang
authors.forename: Chung F
authors.initials: CF
authors.lastname: Wong
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D012984:Software; D013223:Statistics as Topic; D013816:Thermodynamics
chemical_list: D010455:Peptides