May 29, 2012 12:46 PM Summer 2012 Newsletter is Available
Today we release our first newsletter describing our main projects. We will also distribute it at the RNA Society meeting in Ann Arbor.
May 7, 2012 12:45 PM Using New Tools for Predicting 3D Structural Motifs
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.
Nov 7, 2011 12:43 PM RNA Base Triple Paper is Online
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.
Apr 7, 2011 12:42 PM WebFR3D Paper is Online
WebFR3D paper is accepted for publication in the 2011 Webserver Special Issue of Nucleic Acids Research. You can get early access here.
Mar 7, 2011 12:41 PM More Search Examples, Minor Interface Tweaks
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.
Feb 7, 2011 12:40 PM WebFR3D is in Sync with PDB
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.
Dec 10, 2010 12:39 PM Redesigned WebFR3D is Here
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.