New Features in RNA 3D Hub (September 2012)

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 theJmolTools plugin for dynamic retrieval and visualization of 3D structural fragments in Jmol.

Please feel free to get in touch with any feedback.

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.