A news article about BGSU RNA team was featured on BGSU website:
This week we are rolling out an update to WebFR3D, which includes several enhancements:
In the past upgrading FR3D, the computational engine powering WebFR3D, was done fairly rarely, and as a result improvements in FR3D basepair annotations and search algorithms were not making their way to WebFR3D. Now the official FR3D repository is included in WebFR3D as a submodule, which allows for much better control over what version of the software is deployed.
Since the beginning it was possible to use WebFR3D to search non-redundant lists of RNA 3D structures. However, these lists had to be updated manually and this wasn’t done regularly. Now WebFR3D is integrated with the Non-redundant Atlas, which is a part of RNA 3D Hub. The non-redundant lists are automatically updated every week.
[updated: added description of the new features in the Non-redundant Atlas]
This week we are introducing RNA Structure Atlas, which provides a new way of browsing the RNA 3D Hub by PDB.
Each PDB file has its own webpage, for example, here is a summary page for PDB 1S72:
From this page the users can navigate to other webpages where they can:
RNA Structure Atlas integrates the information from various parts of RNA 3D Hub and presents it in a streamlined interface, which can help explore the structural database in a more efficient way.
Work on the documentation is underway. We will provide detailed explanations of the nucleotide id format and all pairwise interaction abbreviations.
Please feel free to get in touch with any feedback.
We are also rolling out an update to the Non-redundant Atlas, a regularly updated collection of non-redundant RNA 3D structures grouped by molecule, organism, and resolution.
The csv files are formatted as follows:
"Equivalence class id","Representative structure","Comma-separated list of the equivalence class members"
Also, the data can be accessed automatically using wget or any other program. For example, here is a sample Python script for downloading the current non-redundant lists: https://gist.github.com/3761913
The Non-redundant Atlas should also feel much snappier than before thanks to a new caching mechanism.
RNA 3D Hub has been updated with new functionality making it easier to explore the RNA 3D Motif Atlas and the Loop Atlas.
New features of the motif pages (for example, the sarcin-ricin motif):
Abstract: This session covers prediction of RNA 3D structure from sequence. Participants will learn about new resources which organize RNA 3D structures and known RNA motifs. Participants will get RNA sequences, fold them using standard programs, and use a new tool called JAR3D to predict the 3D structures of the internal and hairpin loops.
Tutorial level: Introductory/Advanced
Requirements: The intended audience is molecular and systems biologists interested in non-coding RNAs, RNA 3D structure, and RNA function. Participants should bring their own laptops and an interest in RNA structure and function. After an initial overview of RNA 3D structure, the workshop will provide hands-on instruction in the navigation of the author’s website and use of their software.
WebFR3D paper is accepted for publication in the 2011 Webserver Special Issue of Nucleic Acids Research. You can get early access here.
WebFR3D development is continuing with more features coming soon. Let us know what you think about WebFR3D and what is on your wishlist using the contact form.
We have added more examples of geometric WebFR3D searches; now they include sarcin-ricin, triple-sheared, kink-turn, C-loop and T-loop. You can view the search parameters and launch a new search, or examine the precomputed results by clicking on ‘View results’ link in the Help section on the bottom left of the screen.
Fixed an issue with the Jmol applet on the results page overlaying the PDB info popup window. Thank you for pointing this problem out!