News

Equivalence classes organized by Integrated Functional Elements (IFEs) Aug 1, 2017 12:46 PM Today we release our first newsletter describing our main projects. We will also distribute it at the RNA Society meeting in Ann Arbor.

FR3D annotations of RNA basepairs updated Jul 1, 2017 11:00 AM The paper describing the Rutgers-BGSU collaboration to update NDB has been published.

mmCIF files incorporated into representative sets Oct 1, 2016 12:06 PM Today we release our first newsletter describing our main projects. We will also distribute it at the RNA Society meeting in Ann Arbor.

mmCIF files being annotated on our site and NDB Sep 1, 2016 2:46 PM Today we release our first newsletter describing our main projects. We will also distribute it at the RNA Society meeting in Ann Arbor.

Upgrading the BGSU RNA website Feb 13, 2015 12:57 PM Following the recent switch to mmCIF as the main format for 3D structural data distribution, we are upgrading RNA 3D Hub to take advantage of the new data. While this work is in progress, we paused the automatic updates while keeping all previous releases and annotations available.

FR3D Works on Octave Oct 1, 2014 12:56 PM 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.

RNA 3D Structure Course Published Online Oct 1, 2014 12:55 PM 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.

The Nucleic Acid Batabase: New Features and Capabilities Oct 1, 2014 12:55 PM The paper describing the Rutgers-BGSU collaboration to update NDB has been published.

RNA 3D Motif Atlas Paper has been Published Sep 23, 2013 12:53 PM The paper describing the RNA 3D Motif Atlas has been published in RNA.

R3D Align Paper is Available Online May 29, 2013 12:52 PM 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.

Introduction to RNA 3D Hub Oct 20, 2012 12:51 PM 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 Oct 16, 2012 12:51 PM A news article about BGSU RNA team was featured on BGSU website.

WebFR3D Update Oct 14, 2012 12:50 PM This week we are rolling out an update to WebFR3D, which includes several enhancements.

New Features in RNA 3D Hub (September 2012) Sep 18, 2012 12:49 PM This week we are introducing RNA Structure Atlas, which provides a new way of browsing the RNA 3D Hub by PDB.

New Features in RNA 3D Hub (August 2012) Aug 23, 2012 12:47 PM RNA 3D Hub has been updated with new functionality making it easier to explore the RNA 3D Motif Atlas and the Loop Atlas.

Summer 2012 Newsletter is Available May 29, 2012 12:46 PM Today we release our first newsletter describing our main projects. We will also distribute it at the RNA Society meeting in Ann Arbor.

Using New Tools for Predicting 3D Structural Motifs May 7, 2012 12:45 PM 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.

RNA Base Triple Paper is Online Nov 7, 2011 12:43 PM Base triples are recurrent clusters of three RNA nucleobases interacting edge-to-edge by hydrogen bonding. We find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. Given 12 geometric base pair families defined by the Leontis–Westhof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families.

WebFR3D Paper is Online Apr 7, 2011 12:42 PM WebFR3D paper is accepted for publication in the 2011 Webserver Special Issue of Nucleic Acids Research. You can get early access here.

More Search Examples, Minor Interface Tweaks Mar 7, 2011 12:41 PM 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.

WebFR3D is in Sync with PDB Feb 7, 2011 12:40 PM The RNA-containing PDB files are downloaded from PDB on a weekly basis. The new structures should become available for searching in WebFR3D on Sunday of the week when the structures are released. Automatic updating of the non-redundant lists is coming soon.

Redesigned WebFR3D is Here Dec 10, 2010 12:39 PM List of new features: Improved validation of user input. All nucleotides and all chains are checked before the user submits the form, so that non-existent nucleotides cannot be used in queries.