Submit a parsed Tiamat file for analysis
The above submission link is suitable for simulating DNA assemblies in which DNA duplexes are placed freely in 3D space. The link accepts design files that are first prepared with the software Tiamat [7] and then parsed by running the parser locally. The link performs analysis using a finite-element-based modeling framework for DNA with single base-pair resolution. The procedure is demonstrated in the tutorial.
Users of this submission link are kindly requested to cite the following two references:
- K Pan, DN Kim, F Zhang, MR Adendorff, H Yan, M Bathe. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nat. Commun., 5, 5578 (2014).
[ PubMed Article ]
- K Pan, WP Bricker, S Ratanalert, M Bathe. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Res. (2017).
[ Article ]