I am working on the MD simulation of 3D self-assembling nanostructures. But researchers in our group have mainly worked on proteins, small molecules and synthesized polymers. Softwares including schrodinger and material studio are available. But I have not read any references about modeling DNA nanostructures using these two softwares. 3DNA, Nucleic acid builder (NAB) and Namot2 have been reported. Could I use PyMol for modeling? It seems that 3DNA, NAB, Namot2 and PyMol are visualized softwares. Additionally, AMBER is available, too. Should I develop a 3D structural model using those softwares, and then manipulate the model in AMBER?
Dear Lan Mei,
I suggest you to see links and attached files on topic.
http://x3dna.org/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667640/pdf/jove-74-4401.pdf
https://haddock.science.uu.nl/dna/DARTusage.html
https://www.semanticscholar.org/paper/Analyzing-and-building-nucleic-acid-structures-with-Colasanti-Lu/d45ff6f4e93811efffc9417bdaf0e744264765f4
Best regards
How about trying this one?
http://www.biosci.ki.se/groups/ljo/software/nuccyl.html
You can use many different modellers that allow the construction of nucleic acids. They are generally all valid. But, whatever model you want to do, with any modeler, after minimizing it you have to subject it in a molecular dynamics system with your compound immersed in a cage of water to have a model that is reliable. The models made in vacuo with any system, have no reliability. They are just beautiful 3D images.
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