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Author Topic: Can DSSR detect stacking interaction between ligand and nucleic acid  (Read 64 times)

Offline lvelve0901

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Hi Xiangjun,

My new target structure is 1F1T from RCSB. It is a malachite green aptamer with a ligand called N,N'-TETRAMETHYL-ROSAMINE (ROS).
If you go to the PDB website and search for this PDB, you can see there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

Here, I also attach the PDB file and json file that I generated for your convenience.

Best,
Honglue




Offline lvelve0901

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Re: Can DSSR detect stacking interaction between ligand and nucleic acid
« Reply #1 on: November 16, 2017, 11:25:12 pm »
Hi Xiangjun,

Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

Best,
Honglue

Offline xiangjun

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Re: Can DSSR detect stacking interaction between ligand and nucleic acid
« Reply #2 on: November 17, 2017, 09:15:08 am »
Quote
there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

No, in general. This feature is beyong DSSR’s design scope, at least for now. Why not using the result from reported from the RCSB PDB website? It is an ‘authoritative’ resource, isn't it?

Quote
Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

You may find SNAP helpful. Again, do not forget the many other resources/tools in the field.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.