Topics

1

RNA structures (DSSR) / Building G-quadruplexes

« on: April 29, 2025, 12:03:42 pm »

I am writing this code for GQ structure generation from sequence which can be found here https://github.com/sHr3y4s1/GQ-gen. I have just written this for the first G-track but this can be iterated to create more and then building in loops. I have attached an image of the output of this code. I don't know if this is the best way to do it but I am trying to create a basic canonical structure with specific topologies which can be energy minimized with an ion. I was thinking of a similar way for creating circular Z-DNA structures as well.

2

General discussions (Q&As) / Rebuilding Z-DNA

« on: March 13, 2025, 02:10:17 pm »

I was wondering if there is a way to rebuild Z-DNA with rebuild module in the local installation of x3DNA. I know it works for B-DNA and A-DNA and I can make a Z-DNA fiber model as well but I couldn't find a direct way to extend an existing Z-DNA structure. Is there a workaround which I can try? Thank you in advance.