S3EPY: a Sparky extension for determination of small scalar couplings from spin-state
Abstract S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S3E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrated graphical user interface to programs which outputs graphs and the table of determined couplings.
Content Type Journal Article
DOI 10.1007/s10858-009-9392-1
Authors
Petr Novák, Masaryk University National Centre for Biomolecular Research, Faculty of Science KotláÅ?ská 2 611 37 Brno Czech Republic
Lukáš ŽÃ*dek, Masaryk University National Centre for Biomolecular Research, Faculty of Science KotláÅ?ská 2 611 37 Brno Czech Republic
Veronika MotáÄ?ková, Masaryk University National Centre for Biomolecular Research, Faculty of Science KotláÅ?ská 2 611 37 Brno Czech Republic
Petr Padrta, Masaryk University National Centre for Biomolecular Research, Faculty of Science KotláÅ?ská 2 611 37 Brno Czech Republic
AlžbÄ?ta Å*venková, Academy of Sciences of the Czech Republic Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology VÃ*deÅ?ská 1083 142 20 Prague Czech Republic
Libor Krásný, Academy of Sciences of the Czech Republic Laboratory of Molecular Genetics of Bacteria, Institute of Microbiology VÃ*deÅ?ská 1083 142 20 Prague Czech Republic
VladimÃ*r SklenáÅ?, Masaryk University National Centre for Biomolecular Research, Faculty of Science KotláÅ?ská 2 611 37 Brno Czech Republic
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
Bioinformatics. 2011 Mar 3;
Authors: Tamiola K, Mulder FA
SUMMARY: We describe here the ncIDP-assign extension for the popular NMR assignment programme SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of...
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[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...
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[NMR paper] NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by
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Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14147-51
Authors: Pervushin K, Ono A, Fernández C, Szyperski T, Kainosho M, Wüthrich K
This paper describes the NMR observation of 15N---15N and 1H---15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs...
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11-17-2010 11:15 PM
Fully automated high-quality NMR structure determination of small (2)H-enriched prote
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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...
MQ-HNCO-TROSY for the measurement of scalar and residual dipolar couplings in larger
Abstract We describe a novel pulse sequence, MQ-HNCO-TROSY, for the measurement of scalar and residual dipolar couplings between amide proton and nitrogen in larger proteins. The experiment utilizes the whole 2TN polarization transfer delay for labeling of 15N chemical shift in a constant time manner, which efficiently doubles the attainable resolution in 15N dimension with respect to the conventional HNCO-TROSY experiment. In addition, the accordion principle is employed for measuring (J + D)NHs, and the multiplet components are selected with the generalized version of the TROSY scheme...
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A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
F. Gabel, B. Simon, M. Nilges, M. Petoukhov, D. Svergun and M. Sattler
Journal of Biomolecular NMR; 2008; 41(4); pp 199-208
Abstract:
We present the implementation of a target function based on Small Angle Scattering data (Gabel et al. Eur Biophys J 35(4):313–327, 2006) into the Crystallography and NMR Systems (CNS) and demonstrate its utility in NMR structure calculations by simultaneous application of small angle scattering (SAS) and residual dipolar coupling (RDC)...
S3EPY: a Sparky extension for determination of small scalar couplings from spin-state
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