3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: thanhlequoc on March 27, 2017, 10:17:31 pm

Title: Hydrogen bonds between protein and rna in a docked system
Post by: thanhlequoc 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
Title: Re: Hydrogen bonds between protein and rna in a docked system
Post by: xiangjun 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