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Portal name amps-nmr short description

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Portal name amps-nmr short description



Datum24.05.2017
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Portal name


AMPS-NMR

Short description


AMPS-NMR (AMBER-based Portal Server for NMR structures) is a web interface to set up and run calculations with the AMBER package. The interface allows the refinement of NMR structures of biological macromolecules through restrained Molecular Dynamics (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. As an ancillary service, it provides access to a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein–ligand adducts.

The AMPS-NMR grid-enabled web server, originally developed under the WeNMR e-Infrastructure project (www.wenmr.eu) uses resources provided by the European Grid Initiative (EGI) and the associated National Grid Initiatives (NGIs).


Keywords


NMR; structure determination; structural biology; molecular dynamics

URL


http://py-enmr.cerm.unifi.it/access/index/amps-nmr

Grid-enabled


Yes

Cloud-enabled


No

Total number of registered users


300

Number of registered users over 2015


50

Number of user submissions processed over 2015


n.a.

Number of grid/cloud jobs over 2015


8000

Key references


  • Bertini I, Case DA, Ferella L, Giachetti A, Rosato A. A Grid-enabled web portal for NMR structure refinement with AMBER. Bioinformatics. 27:2384-2390, 2011




  • T.A. Wassenaar, M. van Dijk, N. Loureiro-Ferreira, G. van der Schot, S.J. de Vries, C. Schmitz, J. van der Zwan, R. Boelens, A. Giachetti, L. Ferella, A. Rosato, I. Bertini, T. Herrmann, H.R.A. Jonker, A. Bagaria, V. Jaravine, P. Guntert, H. Schwalbe, W.F. Vranken, J.F. Doreleijers, G. Vriend, G.W. Vuister, D. Franke, A. Kikhney, D.I. Svergun, R. Fogh, J. Ionides, E.D. Laue, C. Spronk, S. Jurka, M. Verlato, S. Badoer, S. Dal Pra, M. Mazzucato, E. Frizziero and A.M.J.J. Bonvin WeNMR: Structural Biology on the Grid. J. Grid. Comp., 10, 743-767 (2012).




  • Keywords
  • Total number of registered users
  • Number of grid/cloud jobs over 2015

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