Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A

The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high...

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Bibliographic Details
Main Authors: Manuela Maurer, Stephanie B. A. de Beer, Chris Oostenbrink
Format: Article
Language:English
Published: MDPI AG 2016-04-01
Series:Molecules
Subjects:
OppA
free-energy calculations
free-energy perturbation
molecular dynamics simulations
computational alchemy
thermodynamic integration
GROMOS
Online Access:http://www.mdpi.com/1420-3049/21/4/499

Internet

http://www.mdpi.com/1420-3049/21/4/499

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