CanDo is a code, developed by LCBB at MIT, that applies a finite-element-based modeling framework for DNA with single base-pair resolution. The output from the code is a computational prediction of single- and multi-layer DNA origami structures, including their mean deformed 3D conformation and conformational flexibility.
NUPACK is a software suite, developed by the Pierce Lab at CalTech, that focuses on the design and energetics of nucleic acid systems.
caDNAno is software for design of three-dimensional
DNA origami nanostructures. It was written with the goal of providing a simple and user-friendly interface to facilitate a process that can be complex and error-prone.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. This program is utilized for the visualization of CanDo output files.
VirtualBox is an operating system emulator that allows you to run guest operating systems, e.g. Linux and Windows, within your host system. As most of the scripts being developed in our group utilize opensource codes/software and are themselves coded with a Unix environment in mind, setting up a Linux system would be useful.
Maya is a very powerful suite of design software from Computer Aided Design (CAD) giant AutoDesk. Normally this software costs a small fortune, however as MIT students all you need to do is follow the links to register and you can get a licence for 13 months. Do it...any self respecting engineer should get up to speed with these kinds of design tools and this is a terrific opportunity to do so!