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Software

As part of our research effort we design software tools.


RNA origami design scripts

The scripts were developed to aid the design of the single-stranded RNA origami structures we published in Science in 2014. We have also published a protocol describing the details of the RNA origami design process.

Ligate is a Perl script that can merge several individual 3D RNA motifs within a PDB file into a single RNA structure. You can access the script and example files here: https://github.com/esa-lab/ligate

Trace is a Perl script that can trace a 2D blueprint of a single-stranded RNA origami structure, and output a code that can be used to design sequences in NUPACK that fold the desired RNA origami. You can access the script and example files here: https://github.com/esa-lab/trace

DNA origami design software

In 2008 we developed the SARSE - DNA origami design package. It is made available here as a historical reference. We also published a protocol for DNA origami design of 3D nanostructures using the SARSE software.

The cadnano software has become the standard for DNA origami design, and we have published a tutorial for DNA origami design using the cadnano software.

Protein H-bonds geometry server

bion-server.au.dk/hbonds/

Software news

2016.11.04 | Publication, Software

Book chapter: Computer-Aided Design of RNA Origami Structures

Steffen Sparvath publishes a book chapter describing a tutorial for RNA origami design. The chapter "Computer-Aided Design of RNA Origami Structures" is published in "Methods in Molecular Biology". The book is called "3D DNA Nanostructures" edited by Yonggang Ke and Pengfei Wang.

2014.11.13 | Publication, Software

Book chapter: Computer-Aided Design of DNA Origami Structures

Denis Selnihhin publishes a book chapter describing a tutorial for DNA origami design. The chapter "Computer-Aided Design of DNA Origami Structures" is published in "Methods in Molecular Biology". The book is called "Computational Methods in Synthetic Biology" edited by Mario Andrea Marchisio.

2014.08.15 | Software

RNA design software released

In connection with our paper "A single-stranded architecture for cotranscriptional folding of RNA nanostructures" published in Science, we have made our scripts available at our website. The scripts were used to design the single-stranded RNA origami structures presented in the paper.