MPP Software

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Contents

NUPACK

Analysis and design of nucleic acid molecules and multistranded systems (NUPACK home page).

Multistrand

Simulation of kinetics for multistranded nucleic acid systems at the secondary structure level. (Link coming soon; contact schaeffer at dna.caltech.edu for a pre-release version.)
Multistrand will soon be integrated with the domain-level strand displacement programming environment developed at Microsoft Research by Luca Cardelli and Andrew Phillips (DSD)

Xgrow

Stochastic simulation of tile-based self-assembly (Xgrow home page).

caDNAno

Computer-aided design of DNA origami nanostructures, developed in William Shih's lab at Harvard (caDNAno home page). We are developing some extensions to this software that allow for insertion of single-stranded loops. (Link coming soon; contact woo at caltech.edu for more information.)

Nanoengineer

Nanoengineer is a molecular nanotechnology CAD program developed by Nanorex, Inc. (Nanrex home page). Rothemund consulted on the DNA origami and structural DNA nanotechnology features.

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