Chess2FLYA

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.