Chess2FLYA: Difference between revisions
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* [[XEASY]] chemical shift list (.prot) with the mean values and standard deviations from 1D shift statistics statistics | * [[XEASY]] chemical shift list (.prot) with the mean values and standard deviations from 1D shift statistics statistics | ||
* CYANA torsion angle restraint file (.aco) that restricts the backbone of regular A-form RNA | * CYANA torsion angle restraint file (.aco) that restricts the backbone of regular A-form RNA | ||
* CYANA macro file | * CYANA macro file (.cya) to generate hydrogen bond restraints for the nucleotides involved in regular Watson-Crick base-pairs. | ||
With this input, and peak lists from 2D <sup>1</sup>H-<sup>1</sup>H NOESY, <sup>1</sup>H-<sup>1</sup>H TOCSY, and natural abundance <sup>1</sup>H-<sup>13</sup>C HSQC spectra, the FLYA algorithm can automatically assign the H1', H2, H5, H6, and H8 protons and their corresponding | With this input, and peak lists from 2D <sup>1</sup>H-<sup>1</sup>H NOESY, <sup>1</sup>H-<sup>1</sup>H TOCSY, and natural abundance <sup>1</sup>H-<sup>13</sup>C HSQC spectra, the FLYA algorithm can automatically assign the H1', H2, H5, H6, and H8 protons and their corresponding <sup>13</sup>C resonances in double-stranded RNA. | ||
Chess2FLYA was developped by Thomas Aeschbacher, Markus Blatter, and Mario Schubert in the group of Prof. Frédéric Allain at ETH Zürich. | |||
== Availability == | == Availability == | ||
* Chess2FLYA is freely [ | * Chess2FLYA is freely [[Media:chess2flya-1.1bin.tgz|available]]. The current version is Chess2FLYA 1.1 (05.04.2015). | ||
== Documentation == | == Documentation == | ||
* [[Media: | * [[Media:README150409.pdf|README]] file | ||
== References == | == References == | ||
* Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics | * Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Aeschbacher13-RNAFLYA.pdf .] [http://dx.doi.org/10.1093/nar/gkt665 Nucl. Acids Res. 41, e172 (2013)] | ||
[http://www.bpc.uni-frankfurt.de/guentert | |||
:''Please cite this paper in reports or publications of results obtained with Chess2FLYA.'' | :''Please cite this paper in reports or publications of results obtained with Chess2FLYA.'' | ||
Latest revision as of 13:11, 9 April 2015
Chemical shift statistics to FLYA
Chess2FLYA is a C++ program that uses RNA secondary structure information in the connectivity table format (.ct file format) and a built-in chemical shift statistics file to generate the following input files for the FLYA automated resonance assignment algorithm implemented in the program package CYANA:
- CYANA sequence file (.seq) with the RNA sequence
- XEASY chemical shift list (.prot) with the mean values and standard deviations from 1D shift statistics statistics
- CYANA torsion angle restraint file (.aco) that restricts the backbone of regular A-form RNA
- CYANA macro file (.cya) to generate hydrogen bond restraints for the nucleotides involved in regular Watson-Crick base-pairs.
With this input, and peak lists from 2D 1H-1H NOESY, 1H-1H TOCSY, and natural abundance 1H-13C HSQC spectra, the FLYA algorithm can automatically assign the H1', H2, H5, H6, and H8 protons and their corresponding 13C resonances in double-stranded RNA.
Chess2FLYA was developped by Thomas Aeschbacher, Markus Blatter, and Mario Schubert in the group of Prof. Frédéric Allain at ETH Zürich.
Availability
- Chess2FLYA is freely available. The current version is Chess2FLYA 1.1 (05.04.2015).
Documentation
- README file
References
- Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucl. Acids Res. 41, e172 (2013)
- Please cite this paper in reports or publications of results obtained with Chess2FLYA.