2014-10-01 FR3D works on Octave

The motif search tool FR3D has been revised to work better with Octave, which runs Matlab code in much the same way that Matlab does.  The new programs can be downloaded from Github at this link and instructions for running it can be found at this link.

2014-10-01 RNA 3D structure course published online

Prof. Zirbel taught a workshop course on RNA 3D structure while on sabbatical visiting Ivo Hofacker’s group at the University of Vienna.  The contents of the course are available online at this link.  It introduces the RNA nucleotides, RNA basepairs including non-Watson-Crick basepairs, RNA base stacking, base-phosphate interactions, anti and syn conformation of the backbone, RNA motifs, sequence variability in RNA motifs, and the rudiments of motif searching using FR3D.

2014-10-01 New Publication: The Nucleic Acid Database: New features and capabilities

The paper describing the Rutgers-BGSU collaboration to update NDB has been published:

http://nar.oxfordjournals.org/content/42/D1/D114.long

RNA 3D Motif Atlas paper has been published

The paper describing the RNA 3D Motif Atlas has been published in RNA. If you use the Motif Atlas resource, please cite:

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

Anton I. Petrov, Craig L. Zirbel, and Neocles B. Leontis

RNA October 2013 19: 1327-1340; Published in Advance August 22, 2013, doi:10.1261/rna.039438.113

R3D Align paper is available online [Updated]

F2.medium

The final version of our new paper describing R3D Align webserver has been published by Nucleic Acids Research. The paper appeared in the NAR Web Server Issue in June 2013. Please feel free to use R3D Align and contact us with questions or feedback.

Introduction to RNA 3D Hub

Take a look at the RNA 3D Hub demo presented by Anton Petrov at the Rustbelt RNA Meeting on October 20, 2012.

BGSU RNA team in the news

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

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

WebFR3D update

This week we are rolling out an update to WebFR3D, which includes several enhancements:

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

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

New features in RNA 3D Hub (September 2012) [Updated]

[updated: added description of the new features in the Non-redundant Atlas]

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.

 

New features in RNA 3D Hub (August 2012)

RNA 3D Hub has been updated with new functionality making it easier to explore the RNA 3D Motif Atlas and the Loop Atlas.

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

The RNA 3D Hub Loop Atlas contains all internal, hairpin or 3-way junction loops found in all RNA-containing 3D structures as of February 2012 (in the future the Loop Atlas will be updated regularly). Each loop has its own webpage. For example, a sarcin-ricin loop IL_1JBR_002 has the following stable url: http://rna.bgsu.edu/rna3dhub/loops/view/IL_1JBR_002.
Now these pages include several new features:
  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.
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