title: MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
abstract: CONCLUSIONS
  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).
  
  
  BACKGROUND
  http://mmb.irbbarcelona.org/MDWeb; additional information and methodology details can be found at the web site ( http://mmb.irbbarcelona.org/MDWeb/help.php)
authors.affiliation: Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona, Spain.
authors.forename: Adam
authors.initials: A
authors.lastname: Hospital
authors.forename: Pau
authors.initials: P
authors.lastname: Andrio
authors.forename: Carles
authors.initials: C
authors.lastname: Fenollosa
authors.forename: Damjan
authors.initials: D
authors.lastname: Cicin-Sain
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Josep Lluís
authors.initials: JL
authors.lastname: Gelpí
mesh_terms: D006801:Humans; D020407:Internet; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D009696:Nucleic Acids; D011506:Proteins