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Software

As part of our research effort we design software tools.


RNAO 2.0 design package

The RNA origami design package version 2.0 contains RNAbuild to allow automated construction of 3D models from 2D blueprints, Revolvr to facilitate efficient sequence design of large RNA nanostructures, and a set of utility scripts to analyze folding quality and topology. Read the latest version of our tutorial material. Try the programs at our webserver. Download the latest version at our github repository.

RNAO 1.0 design package

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/ligateTrace 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 It is made available here as a historical reference.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/

PPfold

Parallel Phylogenetic folding algorithm for RNA secondary structure

Webserver

SARSE: Semi-Automated RNA Sequence Alignment Editor

http://sarse.ku.dk

AU Labbook

AU Labbook is a web-based system for research documentation and collaboration (found at labbook.au.dk) based on the Confluence system. We established the system in 2007 and have been developing it over the years into a University-wide solution for documenting research supported and run by the Faculty of Science and Technology. As of November 2018 there are approximately 1500 users with 2000 views and 400 edits per working day. The decision to use the system for research documentation lies with the VIP of a research group. By choosing a common platform for research documentation it becomes easier for the individual researcher to follow the rules for responsible conduct of research. Here is the official description of AU Labbook.

Biomolecular Nanodesign Database (BIOND)

The Biomolecular Nanodesign Database (BIOND) is being developed to facilitate the sharing of DNA, RNA and protein designs as they are developed by the scientific community and possibly companies. The main concept is to share designs so that we can build upon other peoples work and thus accelerate the development of biomolecular design technology. BIOND is also meant to encourage good documentation of designer structures by rating the "quality" and "popularity" of the individual designs. The database is meant to be open for people to share new designs, but also contain a curated core with DB-IDs to facilitate reference in research articles.

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.