Is there a direct option/function to find amino acid atoms around base pairs, i.e. protein contacts with DNA/RNA? Or can you suggest a way to combine various 3DNA functions to approach this?
No, there is no such as an option in 3DNA to find contacts of amino-acids with nucleotides, as the "-w" option for waters.
In the same paper, I also mentioned:
The interactions with users from different backgrounds have given us the incentive to adapt the programs for further applications in related fields, for example, RNA structure-motif identification and alignment, structural analysis of DNA–protein complexes and modeling RNA folds. The reference-frame-based description of three-dimensional spatial geometry makes the methodology and algorithms in 3DNA directly applicable to these problems and treats them in a rigorous and consistent fashion
Specifically, for one of my current research projects, I have written a program named SNAP (Structure of Nucleic Acids and Protein) which has this functionality, among other things. However, SNAP is not part of 3DNA: I am currently beginning to write a manuscript on this topic, and will make it available in due time.
Of course, if you check the literature, there are many ways to find the contacts between aa with nt: e.g., Kono/Sarai, Pabo + Siggers/Honig, and Luscombe/Thornton.
Xiang-Jun
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PS. As a side note, in 3DNA Nucleic Acids Research, 2003 (Vol. 31, No. 17, 5108--5121), I mentioned the following:
Since the six base pair parameters uniquely define the relative position and orientation of two bases, they can be used to reconstruct the base pair. Moreover, the parameters provide a simple mechanism for classification of structures (55) and database searching (X.-J. Lu, Y. Xin and W.K. Olson, unpublished data).
Topic: Find DNA-protien contacts using 3DNA (Read 17323 times)