1. High-throughput automated preparation and simulation of membrane proteins with HTMD
- Author
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Toni Giorgino, Gianni De Fabritiis, Stefan Doerr, João M. Damas, and Gerard Martínez-Rosell
- Subjects
0301 basic medicine ,Computer science ,Lipid Bilayers ,high throughput ,Molecular systems ,Molecular Dynamics Simulation ,01 natural sciences ,03 medical and health sciences ,Molecular dynamics ,Software ,biophysics ,0103 physical sciences ,Animals ,Humans ,Physical and Theoretical Chemistry ,Databases, Protein ,Throughput (business) ,Protocol (object-oriented programming) ,membrane ,Simulation ,Flexibility (engineering) ,computational ,010304 chemical physics ,business.industry ,Membrane Proteins ,Computer Science Applications ,High-Throughput Screening Assays ,030104 developmental biology ,Membrane ,Membrane protein ,Computer architecture ,business - 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 .
- Published
- 2017
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