3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: lvelve0901 on October 18, 2017, 11:35:30 am

Title: FRABASE
Post by: lvelve0901 on October 18, 2017, 11:35:30 am: Hi Xiangjun,

Do you have any idea that how different between DSSR and some online RNA database such as FRABASE in terms of secondary structure identification.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-231

Thanks.

Best,
Honglue
Title: Re: FRABASE
Post by: xiangjun on October 18, 2017, 01:00:29 pm: Hi Honglue,

Please see the FAQ entry "How does DSSR compare with other tools? (http://docs.x3dna.org/dssr-manual.pdf)" in the DSSR User Manual for my thought on such comparisons.

In addition to the above general response, below is a quote from "RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-231)":

Quote
Several dedicated programs, web-accessible servers and databases have been proposed for processing and analysis of the PDB files (c.f. [3]) to study three-dimensional RNA structure. Among them, two particular programs are of general use and of specific importance to our work: 3DNA [4] and RNAView [5]. The first program calculates a complete set of rigid-body parameters that describe the detailed geometry of double helices extracted from the tertiary RNA structures. The second one finds all base pairs and multiplets in the RNA structure and offers the classification of canonical and non-canonical base-pairs. Both programs have been implemented in web-servers [2, 6].

In the current context, it is safe to say: DSSR = 3DNA + RNAview + ...

Xiang-Jun
Title: Re: FRABASE
Post by: lvelve0901 on November 13, 2017, 10:06:40 am: I see.

Thanks.

Best,
Honglue