RNA Base Triple Database Help
Table of contents
2024 release
In February 2024, we generated a single release of the Base Triple Database with a new format. All base triples are listed on the RNA Base Triple spreadsheet. There are tabs for different resolution cutoffs (1.5A, 2.0A, 2.5A, 3.0A). At each resolution, there are two tabs, one that lists each base triple family once, which is called "by_family" and one which lists each base combination within each base triple family, which is called "by_base". There is one additional tab for a small number of intermediate triples, in structures at 2.5A resolution or better.
by_family tabs
- Columns for the Leontis-Westhof interactions made between base 1 and 2, and between base 2 and 3.
- Counts of the number of observed base triples
- Links to two HTML pages to see coordinates
- Online coordinate viewer for all instances
- Online coordinate viewer for typical instances
- Typical instances are ...
by_base tabs
- Columns
- Link to HTML page to see coordinates of all instances from the given family and with the given base combination
- For example, there are 1821 cWW-cSS base triples with base combination GCA. Here the cWW pair is between G and C, and the cSS pair is between C and A.
intermediate triples
- A small number of base triples not consisting of two annotated basepairs were identified in the 2011 paper. We searched for these geometrically and present the instances in this spreadsheet tab.
How the 2024 release was generated
- New FR3D searches
We have created a new version of Fred Search that is oriented towards intelligent search and organization of base triples. Our research levels primarily focus on three levels.
The first is what we call 'family search,' which seeks all instances of a particular interaction (for example cWW_cHW).
Our second level of research focuses on what we call the 'typical instances of the family.' These typical instances represent a small number of similarities and differences appearing between different combinations of bases that form corresponding base triple interactions. This provides, for example, the opportunity to know which type of base can be replaced in a specific interaction by another base.
The third level of search is called 'base combination instances,' which extract different existing groups of base combinations that make up the family interaction. (For example, there is an HTML file that shows all the A, C, and G bases making a cWW_cHW interaction.) For these three levels of search, we have personalized the previous Fred HTML webpage for each element of the group, giving the possibility to visualize the corresponding typical instance when navigating on one of the family pages and also added a link to the variability sequence server……..
About the database
The main page can be accessed at http://rna.bgsu.edu/Triples. The data are organized in two tables: 108 triple families on the left and 64 sequence combinations on the right. If a triple family or a sequence combination has been encountered in the Non-redundant list of RNA 3D structures, then the corresponding cell is colored green. If no instances have been observed in 3D structures, the cells are colored orange.
The numbers in the triple family table (9/36 for cWW-cHW triple family) refer to the number of observed sequence combinations (9 in this case) out of potential sequence combinations (36) that are predicted for this triple family. The maximum number of potential sequence combinations is 64, but in some families certain sequence combinations cannot form due to steric clashes.
The RNA Base Triple Database supports versioning, making it easy to access different releases independently. By default, the current version of the database is loaded (version 1.0 at the time of writing), but previous releases can be selected from the dropdown menu:
Version number is also clearly indicated in the urls of all pages to facilitate referencing, for example:
http://rna.bgsu.edu/Triples/triples.php?version=v1.0 or
http://rna.bgsu.edu/Triples/script.php?family=Triple_cWW_cHW&version=v1.0
Version history
v1.4 (current) - clashes are calculated between bases, sugars and backbones. More improvements in model building. August 20, 2011.
v1.3 - internal test release, new algorithm for backbone placement for model building.
v1.2 - internal test release.
v1.1 - minor modifications of v1.0. Triple_cWW_tSS family is now based on tsS subfamily of tSS base pair. Jan 25, 2011.
v1.0 - based on January 2011 Non-redundant dataset. Jan 15, 2011.
v0.9 - internal test release.
v0.8 - based on May 2010 Non-redundant dataset.
Versions can be compared via an online tool available at http://rna.bgsu.edu/Triples/compare.html
Viewing triple families
1 - the sequence combination may form, but only “near” examples have been observed meaning that one or more constituent basepair is classified as “near” by FR3D (llight-green background). Clicking on the “near” link will display these near instances on the same webpage.
2 - the sequence combination can potentially form, but has never been observed (orange background).
3 - the sequence combination is not expected to form and has never been observed.
4 - the sequence combination is observed (dark green background).
Most elements on the page are clickable. For example, clicking on the number of clashes will bring up interactive KiNG applet, where the clashes are shown as red dots.
Clicking on the number of instances with show all instances using Jmol applet.
Note that the clashes have been calculated only for exemplars and predicted models. Thus, in case 1 on the picture above, the number of clashes refers to the model and not to the near instance. This is due to the fact that it may not be very useful to select a centroid from near instances and calculate its clashes because near instances can be quite diverse.
Both models and exemplars can be superimposed in the Jmol window on the right of the screen by clicking on checkboxes located next to sequence combinations in each cell.
Contact Info
Please email your questions or comments about the website to Craig Zirbel (zirbel@bgsu.edu ).