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
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
J Comput Biol. 2011 Mar;18(3):347-63
Authors: Jang R, Gao X, Li M
Abstract In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow...
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03-10-2011 03:51 PM
[NMR paper] An integrated platform for automated analysis of protein NMR structures.
An integrated platform for automated analysis of protein NMR structures.
Related Articles An integrated platform for automated analysis of protein NMR structures.
Methods Enzymol. 2005;394:111-41
Authors: Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT
Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress...
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11-24-2010 11:14 PM
[NMR paper] Automated analysis of protein NMR assignments and structures.
Automated analysis of protein NMR assignments and structures.
Related Articles Automated analysis of protein NMR assignments and structures.
Chem Rev. 2004 Aug;104(8):3541-56
Authors: Baran MC, Huang YJ, Moseley HN, Montelione GT
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11-24-2010 10:01 PM
Fully automated high-quality NMR structure determination of small (2)H-enriched prote
Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
Related Articles Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
J Struct Funct Genomics. 2010 Aug 24;
Authors: Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT
Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands...
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08-25-2010 02:04 PM
[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Protein Eng. 1996 Nov;9(11):1063-5
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
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08-22-2010 02:20 PM
[Ryan's blog] Is There Hope for Fully Automated Structure Elucidation?- New Article Published
Source: Ryan's blog
Is There Hope for Fully Automated Structure Elucidation?- New Article Published
Computer Assisted Structure Elucidation (CASE) is a major challenge in and of itself. We've been working on this for many, many years and we continue to make huge strides in this area. The technology is sound, the software is being...
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
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