A news article about BGSU RNA team was featured on BGSU website:

http://www.bgsu.edu/offices/mc/page119912.html

1. Seamless integration with FR3D

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.

2. Integration with RNA 3D Hub

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.

3. Other improvements

• Bug fixes related to sending email notifications.
• WebFR3D informational website has been integrated with the rest of the rna.bgsu.edu website.
• All old WebFR3D results should still be available.
• WebFR3D code is now hosted on Github.

Please let us know if you encounter any problems with WebFR3D by using the contact form, by submitting an issue on Github, or by tweeting at RNA 3D Hub.

New website

Geometric Search

Symbolic Search

1. RNA Structure 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:

• view and download pairwise interaction annotations produced by FR3D, including base-pairing, base-stacking, and base-phosphate interactions.
  
• view all internal, hairpin and junction loops found in the 3D structure. Some structures are also annotated with recurrent motifs from the RNA 3D Motif Atlas. In the near future, all structures will be annotated with motifs.
  
• identify similar RNA 3D structures from the non-redundant lists.

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.

RNA Structure Atlas uses Chosen, an excellent javascript plugin, which powers the navigation dropdown list. We also use the JmolTools plugin for dynamic retrieval and visualization of 3D structural fragments in Jmol.

Please feel free to get in touch with any feedback.

2. Non-redundant Atlas

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.

Now it’s possible to download the lists in csv format using the web interface:

The csv files are formatted as follows:

"Equivalence class id","Representative structure","Comma-separated list of the equivalence class members"

For example, http://rna.bgsu.edu/rna3dhub/nrlist/download/0.87/1.5A/csv:

“NR_1.5_23181.1″,”2ASB”,”2ASB”
“NR_1.5_11995.1″,”3HGA”,”3HGA”
“NR_1.5_76588.1″,”397D”,”397D”
“NR_1.5_49442.1″,”2R22″,”2R22″
“NR_1.5_27899.1″,”2Y8Y”,”2Y8Y”
“NR_1.5_93883.1″,”3ND3″,”3ND3,3ND4″

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 Motif Atlas Updates

New features of the motif pages (for example, the sarcin-ricin motif):

1. Similar motifs tab and a new motif comparison tool
   
   Similar motifs are determined by computing minimum linkage between motif groups and shown on the new tab of the motif pages. Motif comparison tool can be launched in a new window by clicking the “Compare” link (example).
   
   The comparison tool shows an interactive heatmap with geometric discrepancies between all instances of the two motifs. When the matrix is clicked, the Jmol window displays the superposition of the corresponding motif instances. If there is a structural conflict preventing some instances from being in the same motif group, then the cells in the heatmap are marked with an “x” and an explanation is provided on hover.
2. History tab
   
   All releases in which the motif is present are listed on the page along with the parent and children motif classes, where applicable.
3. Links to individual loop instance pages. Now all motif pages link to the updated pages for each motif instance.

RNA Loop Atlas Updates

1. General overview of the PDB structure the loop is found in.
2. Information about loop sequence and structure including bulged out bases.
3. Current motif assignment where available.
4. List of nearby proteins found in a 16A neighborhood. To view the proteins in 3D, click “Show neighborhood”. Proteins are colored pink.
5. Similar loops tab, which interactively shows 3D loop superpositions with all similar loops within the geometric discrepancy of 1 A/nucleotide.For each similar loop its motif assignment is also shown (loops belonging to the same motif as the main loop are highlighted in green). If two loops have conflicting structural features, a note explaining the reason behind this conflict is displayed. At this time similar loop comparison is limited to loops that have been assigned to RNA 3D motifs.

Newsletter Summer 2012

“Using New Tools for Predicting 3D Structural Motifs in Non-coding RNAs”

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.

Tutorial materials and handouts

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.

Fixed an issue with the Jmol applet on the results page overlaying the PDB info popup window. Thank you for pointing this problem out!