GeNMR: a web server for rapid NMR-based protein structure determination.
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.
Berjanskii
Mark
M
Department of Computing Science, University of Alberta and National Research Council, National Institute for Nanotechnology, Edmonton, AB, Canada T6G 2E8.
Tang
Peter
P
Liang
Jack
J
Cruz
Joseph A
JA
Zhou
Jianjun
J
Zhou
You
Y
Bassett
Edward
E
MacDonell
Cam
C
Lu
Paul
P
Lin
Guohui
G
Wishart
David S
DS
D000465:Algorithms; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D015203:Reproducibility of Results; D012984:Software