We have developed an approach for simultaneous structure calculation and automatic Nuclear Overhauser Effect (NOE) assignment to solve nuclear magnetic resonance (NMR) structures from unassigned NOESY data. The approach, autoNOE-Rosetta, integrates Resolution Adapted Structural RECombination (RASREC) Rosetta NMR calculations with algorithms for automatic NOE assignment. The method was applied to two proteins in the 15â??20Â*kDa size range for which both, NMR and X-ray data, is available. The autoNOE-Rosetta calculations converge for both proteins and yield accurate structures with an RMSD of 1.9Â*Ã? to the X-ray reference structures. The method greatly expands the radius of convergence for automatic NOE assignment, and should be broadly useful for NMR structure determination.
Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta
Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta
Abstract
We have developed a novel and robust approach for automatic and unsupervised simultaneous nuclear Overhauser effect (NOE) assignment and structure determination within the CS-Rosetta framework. Starting from unassigned peak lists and chemical shift assignments, autoNOE-Rosetta determines NOE cross-peak assignments and generates structural models. The approach tolerates incomplete and raw NOE peak lists as well as incomplete or partially...
nmrlearner
Journal club
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06-19-2014 10:21 PM
Journal Highlight: Automatic assignment of 1H-NMR spectra of small molecules
Journal Highlight: Automatic assignment of 1H-NMR spectra of small molecules
http://www.spectroscopynow.com/common/images/thumbnails/1426b18dc06.jpgA novel data-evaluation procedure for the automatic atom to peak or multiplet assignment of 1H-NMR spectra of small molecules has been developed using a fast and robust expert system.
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nmrlearner
General
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11-18-2013 10:42 PM
[NMR paper] High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.
High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.
Related Articles High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.
J Biomol NMR. 2013 Nov 8;
Authors: Bermel W, Felli IC, Gonnelli L, Ko?mi?ski W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A
Abstract
We present three novel exclusively heteronuclear 5D (13)C direct-detected NMR experiments, namely (H(N-flip)N)CONCACON, (HCA)CONCACON and...
nmrlearner
Journal club
0
11-11-2013 01:30 AM
NOESY assignment of DNA Oligomer
Dear Sir
I am beginner in the field of structural biology of DNA. Is there any paper/book given strategy for sequence specific assignment of short DNA oligomer?
thanks and regards
Surendra
spbiotech08
NMR Questions and Answers
0
05-17-2013 06:06 AM
TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra
TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra
Abstract While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space,...
SAGA: rapid automatic mainchain NMR assignment for large proteins
Abstract Here we describe a new algorithm for automatically determining the mainchain sequential assignment of NMR spectra for proteins. Using only the customary triple resonance experiments, assignments can be quickly found for not only small proteins having rather complete data, but also for large proteins, even when only half the residues can be assigned. The result of the calculation is not the single best assignment according to some criterion, but rather a large number of satisfactory assignments that are summarized in such a way as to help the user identify portions of the sequence...
nmrlearner
Journal club
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08-14-2010 04:19 AM
Mars - automatic backbone assignment of proteins
Link to the program
Mars - robust automatic backbone assignment of proteins.
Jung YS, Zweckstetter M. J Biomol NMR. 2004 Sep;30(1):11-23.
Abstract:
MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar...
Automatic NOESY assignment in CS-RASREC-Rosetta
Linear Mode
