Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBER
Author:
Affiliation:
1. Laboratorio de Integración de Señales Celulares, IHEM, Universidad Nacional de Cuyo, CONICET , Mendoza, Argentina , CP 5500
2. Institut Pasteur de Montevideo , Montevideo, Uruguay, Mataojo 2020, CP 11400
Abstract
Publisher
AIP Publishing LLCMelville, New York
Link
https://pubs.aip.org/books/monograph/chapter-pdf/12805907/9780735425279_003.pdf
Reference25 articles.
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3. Molecular dynamics simulations of membrane proteins and their interactions: From nanoscale to mesoscale;Chavent;Curr. Opin. Struct. Biol.,2016
4. A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics;Dans;J. Chem. Theory Comput.,2010
5. SIRAH: A structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics;Darré;J. Chem. Theory Comput.,2015
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1. Pragmatic Coarse-Graining of Proteins: Models and Applications;Journal of Chemical Theory and Computation;2023-10-03
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