MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
|Title||MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.|
|Publication Type||Journal Article|
|Year of Publication||2012|
|Authors||Hospital, Adam, Andrio Pau, Fenollosa Carles, Cicin-Sain Damjan, Orozco Modesto, and Gelpí Josep-Lluis|
|Date Published||2012 May 1|
|Keywords||Humans, Internet, Molecular Dynamics Simulation, Nucleic Acids, Proteins, Software|
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)