Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo-Reference-Cited by-同舟云学术

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Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo

Published:2022-10 Issue:10 Volume:36 Page:767-779
ISSN:0920-654X
Container-title:Journal of Computer-Aided Molecular Design
language:en
Short-container-title:J Comput Aided Mol Des

Author:

Ge Yunhui,Melling Oliver J.,Dong Weiming,Essex Jonathan W.,Mobley David L.

Funder

National Institutes of Health

Publisher

Springer Science and Business Media LLC

Subject

Physical and Theoretical Chemistry,Computer Science Applications,Drug Discovery

Link

https://link.springer.com/content/pdf/10.1007/s10822-022-00479-w.pdf

Reference40 articles.

1. Laage D, Elsaesser T, Hynes JT (2017) Water dynamics in the hydration shells of biomolecules. Chem Rev 117:10694–10725

2. Maurer M, De Beer SBA, Oostenbrink C (2016) Calculation of relative binding free energy in the water-filled active site of oligopeptide-binding protein A. Molecules 21:499

3. Michel J, Tirado-Rives J, Jorgensen WL (2009) Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization. J Am Chem Soc 131:15403–15411

4. Cournia Z, Allen B, Sherman W (2017) Relative binding free energy calculations in drug discovery: recent advances and practical considerations. J Chem Inf Model 57:2911–2937

5. Ge Y, Baumann H, Mobley D (2022) Absolute binding free energy calculations for buried water molecules. ChemRxiv

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4. WaterKit: Thermodynamic Profiling of Protein Hydration Sites;Journal of Chemical Theory and Computation;2023-04-24

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