Home Page Image      GeNMR (GEnerate NMR structure) is a web server for generating 3D protein structures using NOE-derived distance restraints and NMR chemical shifts. The web server produces an ensemble of PDB coordinates within a period ranging from 20 minutes to 4 hours, depending on protein size, server load, quality and type of experimental information, and selected protocol options. When you publish results of the GeNMR server, please cite the following paper:
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;


Attention:

We had to temporarily revert the server status to public beta due to a large number of changes in the backend scripts that were recently made to accomodate new internet security policies in University of Alberta. Please only use the webserver by submitting the following input files (see more information about file format here):

- Primary sequence in FASTA format
- NOE and H-bond distance restraints in XPLOR format
   and/or
- Chemical shifts in BMRB NMR-STAR 2.1 format
- Proteins with a length above 30 residues

We are working hard to restore server ability to work with other types of input files.


To operate this server:

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.

Examples:

(you could run them to test the server, please do not overdo this)

1) Email Address (required):
2) Self define your input case name(optional): (For example, 1ABC)
3) Select FASTA Sequence file (required): (see allowed formats)
OR
Type (paste) the FASTA Sequence file into the space below (see examples here):

4) Select Chemical Shift Assignment file
(optional, 4) or 5) must input one or both):		 (see allowed formats)
OR
Type (paste) the chemical shift file into the space below (see examples here):

5) Select NOESY file
(optional, 4) or 5) must input one or both):		 (see allowed formats)
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)


 

Current status of the GeNMR server, indicating which jobs have been set to process.


Problems? Suggestions? Please contact feedback



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