title: A Grid-enabled web portal for NMR structure refinement with AMBER.
abstract: BACKGROUND
  The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20-40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols.
  
  
  RESULTS
  We describe a web interface to set up and run calculations with the AMBER package, which we called AMPS-NMR (AMBER-based Portal Server for NMR structures). The interface allows the refinement of NMR structures through rMD. Some predefined protocols are provided for this purpose, which can be personalized; it is also possible to create an entirely new protocol. AMPS-NMR can handle various restraint types. Standard rMD refinement in explicit water of the structures of three different proteins are shown as examples. AMPS-NMR additionally includes a workspace for the user to store different calculations. As an ancillary service, a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein-ligand adducts.
  
  
  METHODS
  AMPS-NMR is embedded within the NMR services of the WeNMR project and is available at http://py-enmr.cerm.unifi.it/access/index/amps-nmr; its use requires registration with a digital certificate.
  
  
  BACKGROUND
  ivanobertini@cerm.unifi.it
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Italy. ivanobertini@cerm.unifi.it
authors.forename: Ivano
authors.initials: I
authors.lastname: Bertini
authors.forename: David A
authors.initials: DA
authors.lastname: Case
authors.forename: Lucio
authors.initials: L
authors.lastname: Ferella
authors.forename: Andrea
authors.initials: A
authors.lastname: Giachetti
authors.forename: Antonio
authors.initials: A
authors.lastname: Rosato
mesh_terms: D020407:Internet; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins