Can combfold predict "Protein-DNA" complexes ?

[28YOGESH]

Thanks for such a great tool, I am just curious to know that will we be able to predict Protein- DNA complexes with combfold.

[ben-shor]

Thanks! You currently can not use CombFold as supplied here for Protein-DNA complexes. However, if you have a large complex with many subunits and a DNA I can offer you this hack:

• Use CombFold to generate the complex
• Use a tool like RosettaFold2NA to predict each subunit with the DNA.
• Manually try to align each subunit predicted with the DNA to the subunit in the CombFold model, and see if any of them makes sense (not too many collisions with the DNA), you can also use confidence from RF2NA.

However, there is still a good chance it will not work, as it may be hard to predict the correct complex conformation when we don't consider the DNA.

Good luck!