A worldwide e-Infrastructure for NMR and structural biology

Professional WeNMR structure calculation service

We now offer professional structure calculation services at special rates for the non-profit biomolecular NMR community. With the service you will get high quality and publication ready structures from your data fast. In addition, by ordering the service you allow us to further support the WeNMR project after the funding ends.

Who does the job?

The work will be performed by Spronk NMR Consultancy, partner in WeNMR and an experienced provider of protein NMR structure determination services. All data provided will be treated as confidential data.

How much does it cost?

The cost depends on the size of the protein and the quality of the data. The price ranges below are for valid for monomeric proteins for which a full set of good quality 3D triple and double resonance data are available (see below), and for which 80% or more of the resonances are assigned.

Price indications are (non-profit institutes only):

  • €1500-2500 for proteins < 50 amino acids
  • €2000-4000 for proteins 50 - 100 amino acids
  • €3000-7500 for proteins 100 - 150 amino acids

For proteins larger than 150 amino acids, multimers, proteins that are not double labeled, and proteins containing non-standard residues or components, prices can be determined after a data check.

What do you get?

We aim to provide you with a publication ready ensemble of structures, refined in explicit solvent and with a structural statistics/validation report. Minor mistakes in assignments we will fix on the fly at no extra costs (The data check does not include a full check of all the assignments). In case there are serious problems with the assignments, we will notify you and discuss what is next and provide guidelines for further improvement of the data.

How does it work?

To offer the services at the above rates we need to be sure that the data is of sufficient quality. So before a service is started, we do a free data check (see below) and tell you whether we can do the project or not and what the exact price will be. The higher the data quality, the faster we can deliver and lower the price will be. If agreed on the price and conditions, we will start the work.

How long does it take?

Depending on the size of the protein, data quality and availability, the estimated delivery time is 1-5 weeks after receiving the full data set.

Data check

For the data check it is best to provide us as much information/data as possible:

  • The protein sequence, including any mutations, special protonation states, disulfide bridges etcetera
  • A full set of consistently calibrated triple and double resonance spectra used for the backbone and side chain assignments and NOESY spectra, such as:
    • 15N-HSQC
    • HNCO
    • HN(ca)CO
    • HNCA
    • HN(co)CA
    • HNCACB
    • CBCA(co)NH
    • HBHA(cbcaco)NH
    • HN(ca)HA
    • CCH(co)NH-Tocsy or CCH-Tocsy
    • H(ccco)NH-Tocsy
    • 15N-NOESY-HSQC
    • 13C-NOESY-HSQC
    • 13C-NOESY-HSQC (aromatic)
  • Chemical shift assignments.
    • If applicable spectrum specific shifts
    • Stereospecific assignments
  • Peak lists used for assignments
  • Information on folding or aliasing of spectra.
  • Any other relevant information (missing signals, multiple conformations, problematic regions etcetera)

Data formats

We prefer data in NMRPipe, Cara, Cyana, Xeasy and Sparky data formats, although we can work with other data as well. When sending data, make sure all files are named correctly and sensibly. A text document describing the data will speed up the process.

Other types of services

If desired, we can provide the full range of NMR structure determination services, including data acquisition, processing and full or partial resonance assignments. You can contact us in case you are interested.

Submit request

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