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Permanent link (DOI): https://doi.org/10.7939/R3QC52

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GeNMR: A web server for rapid NMR-based protein structure determination Open Access

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Author or creator
Berjanskii, M.
Tang, P.
Liang, J.
Cruz, J.A.
Zhou, J.
Zhou, Y.
Bassett, E.
MacDonnell, C.
Lu, P.
Lin, G.
Wishart, D.S.
Additional contributors
Subject/Keyword
databases
macromolecular structure determination
sequences
chemical-shift data
restraints
predictions
C-13
structure generation
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
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 ROSETTAbased 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
.

Date created
2009
DOI
doi:10.7939/R3QC52
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© 2009 The Author(s)
Citation for previous publication
M Berjanskii, P Tang, J Liang, JA Cruz, J Zhou, Y Zhou, E Bassett, C MacDonell, P Lu, G Lin and DS Wishart. "GeNMR: A web server for rapid NMR-based protein structure determination." Nucleic Acids Research 37 (Web Server Issue) (2009): W670-677. DOI: 10.1093/nar/gkp280
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