Skip Navigation



Nucleic Acids Research Advance Access published online on April 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp280
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3083K) Freely available
Right arrow Screen PDF (357K) Freely available
Right arrowOA All Versions of this Article:
37/suppl_2/W670    most recent
gkp280v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Berjanskii, M.
Right arrow Articles by Wishart, D. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Berjanskii, M.
Right arrow Articles by Wishart, D. S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

GeNMR: a web server for rapid NMR-based protein structure determination

Mark Berjanskii1, Peter Tang1, Jack Liang1, Joseph A. Cruz1, Jianjun Zhou1, You Zhou1, Edward Bassett1, Cam MacDonell1, Paul Lu1, Guohui Lin1 and David S. Wishart1,2,3,*

1Department of Computing Science, 2Department of Biological Sciences, University of Alberta and 3National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8

*To whom correspondence should be addressed. Tel: +780 492 0383; Fax: +780 492 5305; Email: david.wishart{at}ualberta.ca

Received February 9, 2009. Revised April 2, 2009. Accepted April 14, 2009.

GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15–25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.