BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

Portal to Wishart Research Group webservers

Click on program name to open web server interface.

PREDITOR: predict φ, ψ, χ1, and ω torsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology.

Reference: Berjanskii MV, Neal S, Wishart DS. PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W63-9.

Visit PREDITOR website for details, help, and usage examples.

Usage:

Select the format of the input file: BMRB NMR-STAR (Example) SHIFTY (Example) FASTA (Example)
Upload chemical shifts 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.
 
Advanded options:
 
Initial steps:
Re-reference chemical shifts Yes No
Only display PDB homologues Yes No
 
Predict dihedral angles using BMRB/SHIFTY input and... Chemical shifts and a PDB homologue (Default)
Chemical shifts only
A PDB homologue only
Chemical shifts and a homologous protein of your choice
- if you use the last option, enter PDB ID or PDB ID & chain letter (Example)
Only homology-based predictions will be run for FASTA input regardless selection of advanced options listed above
 
In addition to predicted angles, output...
X-PLOR/CNS torsion angle restraints Yes No
CYANA/AMBER torsion angle restraints Yes No
Re-referenced chemical shifts Yes No
Predictions of secondary structure using Chemical Shift Index (CSI) Yes No
Predictions of protein flexibility using Random Coil Index (RCI) Yes No
PDB homologues Yes No
 

Problems? Questions? Suggestions? Please contact: Canadian Bioinformatics Help Desk

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

Reference: 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

Visit RCI Website for details, help, and usage examples.

Usage:

Select the format of the input file: BMRB NMR-STAR (Example). SHIFTY (Example)
Upload chemical shifts 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.
 
Advanded options:
Random coil values: Schwarzinger Wang Wishart Lukin
Neighboring residue correction: Schwarzinger Wang
Exclude unassigned residues from analysis: Yes No
Should a correction of terminal end-effects be applied?: Yes No Exclude the first 3 and the last 3 aa
Fill small gaps in distributions of secondary chemical shifts: Yes No
Correct referencing of chemical shifts: No  Yes
Predict secondary structure from chemical shifts: Yes No

SHIFTX2: significantly improved protein chemical shift prediction.

Reference: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and David Wishart. (2011) SHIFTX2: significantly improved protein chemical shift prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. doi: 10.1007/s10858-011-9478-4.

Visit SHIFTX2 website for details, help, and usage examples.

Usage:

  1. Indicate whether the query protein is deuterated.
  2. Fill in information about pH and Temperature (K).
  3. Select the type (all, backbone or proton only) of chemical shift to predict.
  4. Select output format (tabular, comma separated or NMR-STAR format).
  5. Indicate whether to combine results from homology-based method (SHIFTY).
  6. Type in a valid PDB ID or select a local PDB file.
  7. If a input PDB has multiple chains, the first chain will be predicted as default. You can also specify the chain at the end of PDB ID like 2TRXA and 2TRXB
  8. Press the submit button.
Protein is deuterated: Yes No
pH:
Temperature (K):
Select type of chemical shift to be predicted:
Select chemical shift output format:
Combine results with SHIFTY: Yes No
 
PDB ID
OR
Select local PDB file
 

Please contact: [email protected]

CS23D2.0: rapidly generate accurate 3D protein structures using only assigned NMR chemical shifts as input.

Reference: Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G. CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502.

Visit CS23D Website for details, help, and usage examples.

Usage:

  1. Type in a VALID e-mail address. The results will be e-mailed to you.
  2. Upload files (BMRB or SHIFTY format) containing the sequence and chemical shifts of the protein of interest or paste the data into text boxes.
  3. Press the submit button.
E-mail address:
 
FASTA file:
OR:
type (paste) FASTA sequence into the text box below (see examples here):
 
Chemical shifts file:
OR:
type (paste) the chemical shifts into the text box below (see examples here):
 
Number of GAFolder Iterations:
Number of Ensemble Structures Generated:
Ignore exact Matching Structures in Calculation

GeNMR: generate 3D protein structures using NOE-derived distance restraints and NMR chemical shifts.

Reference: Mark Berjanskii, Peter Tang, Jack Liang, Joseph A. Cruz, Jianjun Zhou, You Zhou, Edward Bassett, Cam MacDonell, Paul Lu, Guohui Lin and David S. Wishart. GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Research 2009 37(Web Server issue):W670-W677

Visit GeNMR website for details, help, and usage examples.

Usage:

  1. Type in a VALID email address.
  2. Upload protein primary sequence in FASTA format
  3. Upload NMR chemical shifts in BMRB NMR-STAR 2.1 format
  4. Upload NOE & H-bond distance restraints in XPLOR format
  5. Adjust the number of generated structures. Use 3 for testing your input files. Use 100 for a production run. The size of ensemble will be 20 or the number of generated structures, whichever is less
  6. Adjust parameters of structure generation protocol (e.g. use of exact matching homolog)
  7. Press the submit button. The results will be displayed on the web and emailed to you
Email Address (required):
Self define your input case name (optional): (for example, 1ABC)
 
Select FASTA Sequence file (required): (see allowed formats)
OR
Type (paste) the FASTA sequence into the space below (see examples here):
 
Select Chemical Shift Assignment file: (see allowed formats)
(optional, either chemical shifts or NOESY file or both must be present)
OR
Type (paste) the chemical shift file into the space below (see examples here):
 
Select NOESY file: (see allowed formats)
(optional, either chemical shifts or NOESY file or both must be present)
OR
Type (paste) the NOESY data into the space below (see examples here):
 
Options:
Exclude PDB when selecting homolog (For example, 1ABC;
if more than one, please use space or ',' to separate them.)
OR ignore exact matching structures during the homology modeling step
OR Ab initio when with NOE distance.
Number of structures to generate and select an ensemble from:
(Min. = 3, Max. = 200. Size of ensemble is <= 20)
 

Problems? Questions? Suggestions? Please use feedback form

PROSESS: evaluate and validate protein structures solved by either X-ray crystallography or NMR spectroscopy.

Reference: PROSESS: a protein structure evaluation suite and server; Berjanskii M, Liang Y, Zhou J, Tang P, Stothard P, Zhou Y, Cruz J, Macdonell C, Lin G, Lu P, Wishart DS.; Nucleic Acids Res. Webserver Edition; 2010.

Visit PROSESS website for details, help, and usage examples.

Usage:

  1. Enter your email address
  2. Upload coordinates of a 3D protein model in the PDB format (required)
  3. Upload primary sequence in FASTA format if the 3D model has missing residues
  4. Upload distance restraints with residue numbers matching the 3D model
  5. Upload chemical shifts in BMRB NMR-STAR 2.1 format with residue numbers matching the 3D model
  6. Press the submit button. The results will be displayed on the web in 5-30 min depending on your model.
    If you enter email address, you will also receive an email with links to results.
E-mail address:
Required: select a PDB file on your computer:
OR
Enter PDB accession number:
OR
Copy-paste protein PDB coordinates into the space below (see example):
 
Upload protein sequence in FASTA format:
OR
Copy-paste protein sequence in FASTA format into the space below (see example)
 
Upload distance restraints in XPLOR format:
OR
Copy-paste distance restraints in XPLOR format into the space below (see example)
 
Upload chemical shifts in NMR-STAR 2.1 format:
OR
Copy-paste chemical shifts in NMR-STAR 2.1 format into the space below (see example)

Problems? Questions? Suggestions? Please contact: Canadian Bioinformatics Help Desk

SHIFTCOR: compare, identify, correct and re-reference 1H, 13C and 15N backbone chemical shifts by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure.

Reference: Haiyan Zhang, Stephen Neal and David Wishart (2003) "RefDB: A database of uniformly referenced protein chemical shifts." Journal of Biomolecular NMR, 25: 173-195

Visit SHIFTCOR website for details, help, and usage examples.

Usage:

  1. Type in a valid PDB ID or select a local PDB file.
  2. Select or Paste to a file (BMRB or SHIFTY format) containing the sequence and chemical shifts of the protein of interest.
  3. Press the submit button.
PDB ID:
OR
select local PDB file:
 
Select chemical shift file
(Note: the input file must be in a specific format in order for this form to work. Refer to the SHIFTCOR help.)
OR
type (paste) the file into the space below (see allowed formats):
 

Please contact: [email protected]

Ref-DB: a database of carefully corrected or re-referenced chemical shifts derived from BMRB.

Reference: Haiyan Zhang, Stephen Neal and David Wishart (2003) "RefDB: A database of uniformly referenced protein chemical shifts." Journal of Biomolecular NMR, 25: 173-195

Visit Ref-DB website for details, help, and examples.

Search the RefDB database using a keyword (you may use the boolean search with AND, OR, or '*'.):

Search the RefDB database using a sequence (FASTA format or raw sequence):

Problems? Questions? Suggestions? Please contact: Canadian Bioinformatics Help Desk