QRNAS: software tool for refinement of nucleic acid structures 

 

Program Summary: 

 

QRNAS is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues. 

 

Availability: 

 

QRNAS is free (GNU GPLv3+ license). The software is written in C++. Source code is available for GNU/Linux distributions.
For the compilation of QRNAS, a C++ compiler, such as GNU g++ is required. A bash shell script is provided for the compilation of the package. Download the software from http://genesilico.pl/qrnas/. Unzip the archive, and compile it with the command ./qrnamake sequential to create an executable version of QRNAS. To execute the program use the command …/path/to/QRNAS/QRNA –i input.pdb –o output.pdb where input.pdb is the file to be optimized, and output.pdb is the optimized structure. For more advanced usage of QRNAS, users should consult the README.txt file in the QRNAS package. 

 

Download QRNAS from: 

 

http://genesilico.pl/QRNAS/QRNAS.tgz

 

Datasets available from:

 

http://genesilico.pl/QRNAS/QRNAS_data.tar.gz

 

Bug reports: 

 

All feedback, including bug reports and suggestions for new options to be implemented, should be sent to iamb@genesilico.pl