Related ArticlesGuiding automated NMR structure determination using a global optimization metric, the NMR DP score.
J Biomol NMR. 2015 Aug;62(4):439-51
Authors: Huang YJ, Mao B, Xu F, Montelione GT
Abstract
ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases (15)N-(1)H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
From Mendeley Biomolecular NMR group:
Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al.
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...
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01-29-2016 12:59 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
From Mendeley Biomolecular NMR group:
Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al.
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...
nmrlearner
Journal club
0
09-29-2015 02:39 PM
Guiding automated NMR structure determination using a global optimization metric, the NMR DP score
Guiding automated NMR structure determination using a global optimization metric, the NMR DP score
Abstract
ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to...
nmrlearner
Journal club
0
06-17-2015 08:01 AM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
From Mendeley Biomolecular NMR group:
Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al.
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...
nmrlearner
Journal club
0
10-17-2013 12:49 PM
[NMR paper] Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.
Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.
Related Articles Protein structure prediction using global optimization by basin-hopping with NMR shift restraints.
J Chem Phys. 2013 Jan 14;138(2):025102
Authors: Hoffmann F, Strodel B
Abstract
Computational methods that utilize chemical shifts to produce protein structures at atomic resolution have recently been introduced. In the current work, we exploit chemical shifts by combining the basin-hopping approach to global optimization with...
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02-03-2013 10:22 AM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
From Mendeley Biomolecular NMR group:
Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al.
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...
nmrlearner
Journal club
0
01-09-2013 04:20 PM
[NMR paper] Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
From Mendeley Biomolecular NMR group:
Optimization of the methods for small peptide solution structure determination by NMR spectroscopy
Mol Biol (Mosk) (2010). Volume: 44, Issue: 6. Pages: 1075-1085. A N Istrate, A B Mantsyzov, S A Kozin, V I Pol'shakov et al.
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints...
nmrlearner
Journal club
0
10-12-2012 09:58 AM
[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy].
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Mol Biol (Mosk). 2010 Nov-Dec;44(6):1075-85
Authors:
NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints from NMR spectra. At the same time, short charged peptides play an important role in a number of biological processes, in particular in pathogenesis of neurodegenerative...
Guiding automated NMR structure determination using a global optimization metric, the NMR DP score.
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