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From 2012.igem.org

RNAfold http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

Ape http://en.bio-soft.net/plasmid/ApE.html

3DS Max (for 3d visualization)

After Effects (for animated videos)

Photoshop (por image editing and simple animations)

Protein modeling:

-Rosetta

-Foldit

-MOE: to add hydrogen atoms.

-Autodock: a suite of automated docking tools. This should be useful to evaluate the self-assembly of our monomers.

-Force Field: to calculate potentials between particles.

Protein visualization software: PyMOL, VMD, Chimera.