A worldwide e-Infrastructure for NMR and structural biology

Getting started with XPLOR-NIH

XPLOR-NIH is one of the programs for structure calculations that have been ported to the Grid and are available through the WeNMR web portal. It is a versatile program that can be operated through a command line interface or with scripts in the specific XPLOR language.

Performing structure calculations using NMR data commonly starts with the generation of an extended conformation from a topological description of the macromolecule. For standard components, such as protein, DNA and RNA, this topological description can be easily inferred from the sequence of the building blocks. Distance, orientation and other restraints derived from NMR data can then be added to the topological description and used to drive the system to a folded state using simulated annealing. This annealing step is repeated many times to obtain sufficient statistics regarding the goodness of fit of the structures determined against the experimental data. Since the different annealing runs are independent of each other, they can be easily distributed over multiple CPUs. After the annealing runs have finished, the best structures are usually selected for further refinement, including solvent in the calculations.

The portal uses a design which is different from the HADDOCK portal, and is aimed at more direct user interaction during the process. Users log in with their Grid certificate loaded in the web browser, gaining access to an environment where projects can be started, stored and managed. Structure calculation projects are initiated by filling in a form and providing files for the structures and topological descriptions of the molecules, as well as for the different restraints to be included in the calculations. 

When the structure calculations have finished, the user can view and download the results. In addition, it is possible to select a number of structures for further refinement and characterization using the AMBER package for MD simulations.

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life