We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25Â*kDa that had 27â??98Â*% sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.
[NMR paper] Automated protein structure determination by NMR.
Automated protein structure determination by NMR.
Related Articles Automated protein structure determination by NMR.
J Biomol NMR. 2015 Jul 21;
Authors: Rosato A, Billeter M
PMID: 26195076
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
8 February 2012
Publication year: 2012
Source:Structure, Volume 20, Issue 2</br>
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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...
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02-03-2013 10:13 AM
Advances in automated NMR protein structure determination.
Advances in automated NMR protein structure determination.
Advances in automated NMR protein structure determination.
Q Rev Biophys. 2011 Mar 17;:1-53
Authors: Guerry P, Herrmann T
Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of...
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03-18-2011 06:00 PM
[NMR paper] Protein NMR structure determination with automated NOE assignment using the new softw
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
Related Articles Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
J Mol Biol. 2002 May 24;319(1):209-27
Authors: Herrmann T, Güntert P, Wüthrich K
Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
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11-24-2010 08:49 PM
Automated protein NMR structure determination in solution.
Automated protein NMR structure determination in solution.
Automated protein NMR structure determination in solution.
Methods Mol Biol. 2010;673:95-127
Authors: Gronwald W, Kalbitzer HR
The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has...
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09-14-2010 02:03 PM
[NMR paper] A branch and bound algorithm for protein structure refinement from sparse NMR data se
A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
J Mol Biol. 1999 Jan 29;285(4):1691-710
Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE
We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a...
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data
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