1. caDNAno (.json) file
JSON is the input design file format used for CanDo analysis exported from caDNAno (http://caDNAno.org), which is an open source program that offers rapid prototyping of DNA origami connectivity maps.
2. caDNAno sequence (.csv) file
CSV is the input sequence file format exported from caDNAno.
3. Tiamat (.dna) file
DNA is the input design file format used for CanDo analysis exported from Tiamat (http://yanlab.asu.edu/Resources.html), which is a program that enables lattice-free design of DNA nanostructures.
4. Tiamat sequence (.txt) file
TXT is the input sequence file format exported from Tiamat.
5. CanDo (.cndo) format
We have developed the CNDO format as yet another file format for lattice-free design of DNA nanostructures. CNDO is the input design file format used for CanDo analysis. A detailed description of the CNDO file format is available here. Briefly, CNDO is a text file that contains the identity (A, T, G, C, purine, pyrimidine, unspecified, etc.) of each nucleotide, connectivity between the nucleotides, and position and orientation of each basepair.
6. BILD format
BILD is a text file that lists commands for lines, polygons, and geometric primitives used to generate a VRML model in UCSF Chimera. CanDo provides results to users for download including the 3D solution shape, thermal fluctuations of the solution shape, and lowest normal mode shapes using this format where DNA double helices are represented by cylinders. VRML models can be exported from UCSF Chimera for further uses in other visualization programs. More information about the format is available at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html.
7. PDB format
PDB is a text file that lists for each atom its serial number, name, residue sequence number, residue name, chain identifier, and Cartesian coordinates (in Ångströms). CanDo provides a PDB file to users for download if an atomic model of the uploaded caDNAno design is included with the results. A PDB file can be the input of further full atomistic simulations such as molecular dynamics (MD) simulation. More information about the format is available at http://www.wwpdb.org/docs.html.