A worldwide e-Infrastructure for NMR and structural biology

RCI


 

RCI Website RCI Help Wishart lab

RCI webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH) and estimating values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index. 

Please cite: Mark V. Berjanskii, David S. Wishart (2005) A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts.  Journal of the American Chemical Society, 127 (43), 14970 -14971

 

Basic usage
Select the format of the input file: BMRB NMR-STAR (Example) SHIFTY (Example)
Upload chemical shift file
OR
Paste chemical shifts into the text box below:
IMPORTANT: If a file is selected for upload above, it will be used and content of the text box below will be ignored.
input name:
name is optional and used only when you paste shifts. Please use letters and numbers only, no spaces.
input name will become a part of output filename. If you do not name your input, a random number will be used.
   

 

Advanced options
Random coil values: Schwarzinger (Default)  Wang  Wishart  Lukin 
Neighboring residue correction: Schwarzinger (Default)  Wang 
Exclude unassigned residues from analysis: Yes (Default)  No 
Should a correction of terminal end-effects be applied?: Yes (Default)  No  Exclude the first 3 and the last 3 aa 
Fill small gaps in distributions of secondary chemical shifts: Yes (Default)  No 
Correct referencing of chemical shifts: No (Default)  Yes 
Predict secondary structure from chemical shifts: Yes (Default)  No 
   

 

 

Problems? Questions? Suggestions? Please contact: Mark Berjanskii or the Canadian Bioinformatics Help Desk

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Cite WeNMR

 
Usage of the WeNMR portals should be acknowledged in any publication:
 
"The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project, the International Desktop Grid Federation (IDGF) with its volunteers and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities. "
 
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.

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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