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Author Topic: Hydrogen bonds between protein and rna in a docked system  (Read 866 times)

Offline thanhlequoc

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Hydrogen bonds between protein and rna in a docked system
« on: March 27, 2017, 10:17:31 pm »
Hi everyone,
I have a quick question about hydrogen bonds-can the program find hydrogen bonds between protein and rna (a docked system)? I have tried using get-hbonds command. However, it only gives me hydrogen bonds in rna-not between protein and rna.
Thanks,
Thanh Le

Offline xiangjun

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Re: Hydrogen bonds between protein and rna in a docked system
« Reply #1 on: March 27, 2017, 11:14:31 pm »
Quote
it only gives me hydrogen bonds in rna-not between protein and rna.

By default, the DSSR --get-hbond option outputs only H-bonds within nucleic acids. You can get additional protein-RNA H-hbonds by specifying --get-hbond=at-interface.

As mentioned several times in the Forum, the H-bond identification algorithm in DSSR (and SNAP) has been designed to make DSSR fully self-contained. While it fulfills its role well, it may not be as sophisticated as dedicated programs such as HBPLUS and HBExplore. Please keep this (possible) limitation in mind.

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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.