Introduction to RNA 3D Hub

A demo of RNA 3D Hub, a new resource for RNA Biology available at http://rna.bgsu.edu/rna3dhub

Presented at the Rustbelt RNA Meeting 2012
http://www.rustbeltrna.org/2012

Transcript

1. October 20, 2012 - Rustbelt RNA Meeting - Dayton, OH RNA 3D Hub: an Online Resource for RNA Structural Bioinformatics Anton Petrov, Craig Zirbel, Neocles Leontis Bowling Green State University rna.bgsu.edu
2. Putting useable structural information in the hands of RNA biologists
3. 625 1,250 1,875 2,500 RNA-contiaining 3D structures 1978 1993 2000 2007 2012 RNA-containing 3D structures
4. Protein Data Bank contains many redundant structures Which structure should one study?
5. Dozens of 23S E. coli rRNA structures + 27 more 3I1Z 3I1S 3I21 3I1Q 3I1O 3I1M 3DF3 3DF1 2Z4M 2Z4K 2VHP 2VHO 2QP0 2QOY 2QOW 2QOU 2QBJ 2QBH 2QBF 2QBD 2QBB 2QB9 2QAN 2QAL 2I2U 2I2P 2AW7 2AVY 1VS7 1VS5
6. 23S E. coli rRNA equivalence class + 26 more 2AW7 - representative structure
7. Non-redundant lists of RNA structures
8. • 3D structures grouped by organism, sequence and 3D structure similarity • A representative is selected for each class based on structure quality considerations • Regular automatic updates • Unique and stable ids • Versioning system Non-redundant lists of RNA 3D structures rna.bgsu.edu
10. Representative structure
11. Exploring your favorite structure
13. Basepair interactions
14. RNA 3D motifs found in this structure
15. Instances of a recurrent RNA 3D motif from the Motif Atlas
16. RNA 3D Motif Atlas • Extract RNA 3D motifs from a non-redundant list of 3D structures • Cluster by geometric similarity • All instances of the same motif have the same non-Watson-Crick base pairing pattern • A motif can have instances with different number of nucleotides and different sequences • Unique and stable ids • Versioning system
17. What if there is no 3D structure of your favorite molecule?
18. JAR3D inferring RNA 3D motifs in sequences Accepts single or multiple sequences with or without secondary structure
19. Predicted motifs from the Motif Atlas rna.bgsu.edu
20. RNA 3D Hub Databases: 1. RNA Structure Atlas 2. Non-redundant lists of RNA 3D structures 3. RNA 3D Motif Atlas 4. RNA Base Pair Catalog 5. RNA Base Triple Database Web applications: 1. JAR3D - predicting RNA 3D motifs in sequences 2. WebFR3D - searching RNA 3D structures 3. R3DAlign - global superposition of RNA 3D structures
21. rna.bgsu.edu PDB/NDB: Helen Berman John Westbrook Saheli Ghosn Buvna Narayanan Alumni: Jesse Stombaugh Ryan Rahrig Amal Abu Almakarem Irina Novikova Lab members: Neocles Leontis Craig Zirbel Blake Sweeney James Roll Emil Khisamutdinov Anton Alenko Steve Dinda