A Case Study of Scoring and Rescoring in Peptide Docking

Zunnan Huang; Chung F. Wong

doi:10.1007/978-1-61779-465-0_18

A Case Study of Scoring and Rescoring in Peptide Docking

Zunnan Huang, Chung F. Wong

University of Missouri-St. Louis

Research output: Contribution to journal › Article › peer-review

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 ) = 4 r ) 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 in Yersinia pestis as an example.

Original language	American English
Journal	Methods of Molecular Biology
Volume	819
DOIs	https://doi.org/10.1007/978-1-61779-465-0_18
State	Published - Jan 1 2012

Keywords

CHARMM
Distance-dependent dielectric model
Energy rescoring
Generalized Born model
MMTSB Tool Set
Simulated annealing
YopH inYersinia pestis
ptraj

Disciplines

Computer Sciences
Bioinformatics

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Cite this

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KW - Distance-dependent dielectric model

KW - Energy rescoring

KW - Generalized Born model

KW - MMTSB Tool Set

KW - Simulated annealing

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KW - ptraj

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JO - Methods of Molecular Biology

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ER -

A Case Study of Scoring and Rescoring in Peptide Docking

Abstract

Keywords

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