Structure
Volume 20, Issue 2, 8 February 2012, Pages 227-236
Journal home page for Structure

Ways & Means
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

https://doi.org/10.1016/j.str.2012.01.002Get rights and content
Under an Elsevier user license
open archive

Summary

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.

Highlights

► Automated assignment and structure calculation from NMR NOESY spectra were assessed ► Routine, fully automated determination of protein structures is feasible ► Good stereochemical and geometric quality alone does not indicate structure accuracy

Cited by (0)

19

Present address: Biomolecular Dynamics/Theoretical Biophysics, Technische Universität München, Munich, Germany