A worldwide e-Infrastructure for NMR and structural biology

Structure Calculation Software

CS-ROSETTA

CS-ROSETTA is a protocol which generates 3D models of proteins, using only the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts as input. Based on these parameters, CS ROSETTA uses a SPARTA-based selection procedure to select a set of fragments from a fragment-library (where the chemical shifts and the 3D structure of the fragments are known). The fragments are assembled using the ROSETTA protocol. The generated models are rescored based on the difference between the back-calculated chemical shifts of the generated models and the input chemical shifts. Go to the service >>

CS-ROSETTA3

CS-ROSETTA3 is a new implementation of the CS-ROSETTA serve (above) making using of Rosetta version 3.0 and a new fragment picker. This new server is described in Schot et al. J. Biomol. NMR (2013). Go to the service >>

ARIA

ARIA (Ambiguous Restraints for Iterative Assignment) is a software package for automated NOE assignment and NMR structure calculation. It uses an iterative structure calculation scheme and the final refinement in explicit water improves the quality of the calculated structures. Go to the service >>

CYANA

CYANA allows for automated NMR structure calculation. Given a sufficiently complete list of assigned chemical shifts and one or several NOESY spectra, the assignment of the NOESY cross-peaks and the three-dimensional structure of the protein in solution can be calculated automatically. Go to the service >>

UNIO

The UNIO program enables you to perform automated NMR data analysis for 3D protein structure determination. It includes data analysis algorithms for all parts of an NMR structure determination process ranging from backbone and side-chain assignment to automated NOE assignment and structure calculation. Go to the service >>

Xplor-NIH

Xplor-NIH allows you to run NMR structure calculations with NOE, dihedral angle and paramagnetic restraints on the WeNMR grid infrastructure. Go to the service >>

CcpNmr WMS

CcpNmr WMS is  Workflow Management System that serves as a joint interface for launching NMR structure calculations. Data selection is simple and unified, using CCPN data projects, and multiple programs can be submitted from a single input data set. The program is currently in alpha test, and supports launching calculations on the Cyana, Unio, and CS-Rosetta WeNMR services, and on the CCPNGrid Aria server. Go to the service >>

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