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J Chem Theory Comput. 2017 Sep 12;13(9):4003-4011. doi: 10.1021/acs.jctc.7b00480. Epub 2017 Aug 4.

High-Throughput Automated Preparation and Simulation of Membrane Proteins with HTMD.

Author information

1
Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra , Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain.
2
Institute of Neurosciences, National Research Council of Italy (IN-CNR) , 35127 Padua, Italy.
3
Acellera , Barcelona Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain.
4
Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluis Companys 23, Barcelona 08010, Spain.

Abstract

HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of HTMD for the preparation of a molecular dynamics simulation starting from PDB structures, building the system using well-known force fields, and applying standardized protocols for running the simulations. We demonstrate the framework's flexibility for high-throughput molecular simulations by applying a preparation, building, and simulation protocol with multiple force-fields on all of the seven hundred eukaryotic membrane proteins resolved to-date from the orientation of proteins in membranes (OPM) database. All of the systems are available on www.playmolecule.org .

PMID:
28723224
DOI:
10.1021/acs.jctc.7b00480
[Indexed for MEDLINE]

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