Can I predict the interaction between nucleic acid structure (eg. G-quadruplex) and protein structure (eg. G-quadruplex helicase) based on their 3D sturcture (*PBD files)? Wether the "AutoDock" can handle the question?
Jamison Drew Law
Hello Yuxuan, you can try using AlphaFold3, Chai-1, ProteinX, and Boltz-1 to generate a structure between the nucleic acid and protein of interest. You can also try pyDockDNA, HADDOCK, HDOCK, etc. See the following publication: https://www.sciencedirect.com/science/article/abs/pii/S0959440X24001829. Good luck!
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Alexander Tischer
I´m adding PyRx to what Jamison Drew Law wrote (https://pyrx.sourceforge.io/). Whether any of these predictions are meaningful is a different issue. So, be careful when interpreting it.
Best regards.
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