AI Article Synopsis
- HTMD is a scientific platform designed to enhance research in molecular systems through simulation.
- The paper outlines HTMD's capabilities for preparing molecular dynamics simulations using PDB structures and various force fields.
- The framework was applied to all 700 eukaryotic membrane proteins from the OPM database, with the systems accessible at www.playmolecule.org.
Article 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 .
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| http://dx.doi.org/10.1021/acs.jctc.7b00480 | DOI Listing |
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