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

2012; Oxford University Press; Volume: 28; Issue: 9 Linguagem: Inglês

10.1093/bioinformatics/bts139

1367-4811

Adam Hospital, Pau Andrio, Carles Fenollosa, Damjan Cicin-Sain, Modesto Orozco, Josep Lluis Gelpí,

Mass Spectrometry Techniques and Applications

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 (http://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: http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site (http://mmb.irbbarcelona.org/MDWeb/help.php) Contact: gelpi@ub.edu; modesto.orozco@irbbarcelona.org Supplementary information: Supplementary data are available at Bioinformatics online.