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ShiftRefiner is a webserver for refining protein structures with NMR chemical shifts. The method employs biased quenched molecular dynamics, a multi-criterion genetic algorithm, several knowledge-based scoring functions, and structural information derived from NMR chemical shifts.

Reference: Protein Chemical Shift Refinement on the Web, Mark Berjanskii, David Arndt, Noor Hafsa, and David S. Wishart; (Submitted).

To operate this server:

1) Enter your email address (Optional)
2) Upload coordinates of a 3D protein model in the PDB format (Required)
3) Upload chemical shifts in BMRB NMR-STAR 2.1 or Shifty or NEF formats with residue numbers matching the 3D model (Required)
4) Upload distance restraints with residue numbering matching the 3D model (Optional)
5) Upload dihedral restraints in XPLOR-NIH format with residue numbers matching the 3D model (Required)
5) Press the submit button. The results will be displayed on the web in 1-72 hours depending on your model.
If you enter email address, you will also receive an email with links to results.
6) Print ShiftRefiner results as soon as you receive email notification that your ShiftRefiner job is finished.
ShiftRefiner job files are stored on the server for 3 days.

Important!!!
- Your PDB file, NOE file, and chemical shift file must have identical residue numbering.
- Residue numbering for sub-units of dimers, tetramers, and other multimers must not overlap.
- Chemichal shifts of sub-units must be combined into a single list in NMR-Star 2.1 format
with combined primary sequence entries.
- If you submit an ensemble, the minimal size of an ensemble should be 3 models.

Example to test the server:

(Press the "Get example" button and press "Submit")


Human ubiquitin, 76 residues, monomeric, coordinate error with respect to the reference model (PDB ID id 1UBQ) is 2.0A



1) Optional: Enter your email address:
If you choose not to enter an address, a link will be generated and a tracking page will show you the status of your job



2) Required: Select a PDB file on your computer:
(Find format description here)



OR

Enter PDB accession number
(Please specify the chain e.g. 1UBQA (1UBQ chain A), If not specified, first chain will be processed)

OR

Copy & paste protein PDB coordinates into the space below:
(Find format description here)




3) Required: Upload chemical shifts. Also, select BMRB NMR-STAR 2.1 or NEF format below the text box.
(Find format description here)



OR

Copy & paste chemical shifts in BMRB NMR-STAR 2.1 or NEF formats into the space below:
(Find format description here)

Format of chemical shift file:



4) Optional: Upload distance restraints in XPLOR format:
(Find format description here)



OR

Copy & paste distance restraints in XPLOR format into the space below:
(Find format description here)




5) Optional: Upload dihedral restraints in XPLOR format:
(Find format description here)



OR

Copy & paste dihedral restraints in XPLOR format into the space below:
(Find format description here)



6 ) Optional: Upload secondary structure file in GeNMR format:
(Find format description here)



OR

Copy & paste secondary structure in GeNMR format into the space below:
(Find format description here)





Advanced options:

Simulation time:

Wall-time (hours)

Number of independent simulations:

Simulations