MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

TitleMDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Publication TypeJournal Article
Year of Publication2012
AuthorsHospital, Adam, Andrio Pau, Fenollosa Carles, Cicin-Sain Damjan, Orozco Modesto, and Gelpí Josep-Lluis
JournalBioinformatics
Volume28
Pagination1278-9
Date Published2012 May 1
ISSN1367-4811
KeywordsHumans, Internet, Molecular Dynamics Simulation, Nucleic Acids, Proteins, Software
Abstract

SUMMARY: MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database (https://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform has two ways of access, a set of web-services based on the BioMoby framework (MDMoby), programmatically accessible and a web portal (MDWeb).

AVAILABILITY: https://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( https://mmb.irbbarcelona.org/MDWeb/help.php)

DOI10.1093/bioinformatics/bts139