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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
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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
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.