Article
A Case Study of Scoring and Rescoring in Peptide Docking
Methods of Molecular Biology
(2012)
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.
Keywords
- Simulated annealing,
- Distance-dependent dielectric model,
- Generalized Born model,
- YopH inYersinia pestis,
- Energy rescoring,
- CHARMM,
- MMTSB Tool Set,
- ptraj
Disciplines
Publication Date
January 1, 2012
DOI
10.1007/978-1-61779-465-0_18
Citation Information
Zunnan Huang and Chung F. Wong. "A Case Study of Scoring and Rescoring in Peptide Docking" Methods of Molecular Biology Vol. 819 (2012) p. 269 - 293 Available at: http://works.bepress.com/chung-wong/17/