Blind testing of routine, fully automated determination of protein structures from NMR data.
The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.
Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy. rosato@cerm.unifi.it
Antonio
A
Rosato
James M
JM
Aramini
Cheryl
C
Arrowsmith
Anurag
A
Bagaria
David
D
Baker
Andrea
A
Cavalli
Jurgen F
JF
Doreleijers
Alexander
A
Eletsky
Andrea
A
Giachetti
Paul
P
Guerry
Aleksandras
A
Gutmanas
Peter
P
Güntert
Yunfen
Y
He
Torsten
T
Herrmann
Yuanpeng J
YJ
Huang
Victor
V
Jaravine
Hendrik R A
HR
Jonker
Michael A
MA
Kennedy
Oliver F
OF
Lange
Gaohua
G
Liu
Thérèse E
TE
Malliavin
Rajeswari
R
Mani
Binchen
B
Mao
Gaetano T
GT
Montelione
Michael
M
Nilges
Paolo
P
Rossi
Gijs
G
van der Schot
Harald
H
Schwalbe
Thomas A
TA
Szyperski
Michele
M
Vendruscolo
Robert
R
Vernon
Wim F
WF
Vranken
Sjoerd de
Sd
Vries
Geerten W
GW
Vuister
Bin
B
Wu
Yunhuang
Y
Yang
Alexandre M J J
AM
Bonvin
D057205:Automation, Laboratory; D003627:Data Interpretation, Statistical; D001330:Electronic Data Processing; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012107:Research Design; D012984:Software
D011506:Proteins