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Questions and answers > RNA structures (DSSR)
Can DSSR detect nucleic acid ligand interaction
lvelve0901:
Hi Xiangjun,
I am just curious whether DSSR can detect something like RNA and ligand/metal interaction in a PDB file.
For example, list all the hydrogen bond between RNA and ligand?
Best,
Honglue
xiangjun:
--- Quote ---list all the hydrogen bond between RNA and ligand?
--- End quote ---
Do you have a concrete example of such listing?
Xiang-Jun
lvelve0901:
For example, in the dssr, there is a --get-hbond option. It will output all the H-bonds within two nucleotide and it gives you the distance, donor and acceptor etc., but I guess that only applies for nucleic acid. There is no way to detect H-bond between for example protein-and nucleic acid in current DSSR, right?
If not, do you have any suggestion of any software which can do something like parse the interactions between protein/peptide/ligand and nucleic acids.
Really appreciate your help.
Best,
Honglue
xiangjun:
The DSSR --get-hbond option is more capable than it appears. In its default setting, DSSR only outputs H-bonds between nucleotides. Combined with the --json option, more H-bonds are avaible. Have a try and REPORT back if that fits your needs.
Of course, there are numerous other dedicated tools/resources you may find better-suited for your project.
Xiang-Jun
lvelve0901:
Gotcha, I realized that Json file actually has what I need in the 'hbonds' section.
Also, is there also a section for metal in the pdb file. For example, how many metal-RNA interaction in the PDB file?
Best,
Honglue
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
