A Case Study of Scoring and Rescoring in Peptide Docking

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.