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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.
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Hi shr,
I've split your response from the thread "Rebuilding circular Z-DNA (http://forum.x3dna.org/index.php?topic=1045.0)" into its own thread for better organization and discussion.
It a nice start with the first G-tetrad. Please add more features to your GQ-gen.py script so it can at least build a complete G-quadruplex structure. I'll chime in with some suggestions to your project, while I'm working on adding proper Z-DNA backbone to DSSR-enabled models.
Best regards,
Xiang-Jun
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Hi shr,
Following the discussion in the previous thread on "Rebuilding circular Z-DNA (http://forum.x3dna.org/index.php?topic=1045.0)", as quoted below:
In addition to Z-DNA, I also work on other non-canonical DNA structures, particularly G-quadruplexes (G4s). I’m developing a method to construct ideal G-quadruplex models from sequence data by first arranging guanine bases into tetrads, then building in the backbone and loop regions.
I am glad to hear about your work on G-quadruplexes. Actually, I have recently revised the G4 module in DSSR, fixed existing bugs, and added new features. The g4.x3dna.org (http://g4.x3dna.org) website has undergone a complete overhaul, enabling users to upload their own structures for dynamic G4 analysis. Additionally, the DSSR-G4DB database is being actively updated on a weekly basis as new PDB entries are added. See the four blog posts comparing DSSR with other related analysis tools on G-quadruplexes: ASC-G4 (https://x3dna.org/highlights/g-quadruplex-notes-on-asc-g4), Webba da Silva nomenclature (https://x3dna.org/highlights/g-quadruplex-notes-on-the-webba-da-silva-nomenclature), ElTetrado and related tools (https://x3dna.org/highlights/g-quadruplex-notes-on-eltetrado-and-related-tools), and CIIS-GQ (https://x3dna.org/highlights/g-quadruplex-notes-on-ciis-gq).
Moveover, I am also interested in modeling G-quadruplexes, taking G-tetrad as the building block. There are quite a few other threads in DSSR I'd like to pursue further in the future. I'd certainly like to hear more about your approach on modeling G-quadruplex.
I dug into the code of DSSR for modeling G-quadruplexes, and found the following experimental (and undocumented) features. DSSR can model G-quadruplexes using G-tetrad as the building block, and allows users to specify the number of G-tetrads and twist angle (among other things). See below for two examples: one with 3 layers of G-tetrads and 0 degrees of twist angle, and other with 6 layers and twist=36, respectively.
Best regards,
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University