Introduction to RNA 3D Hub

45ce46ede83b75d073e172b058a8d250?s=47 Anton Petrov
October 20, 2012

Introduction to RNA 3D Hub

A demo of RNA 3D Hub, a new resource for RNA Biology available at

Presented at the Rustbelt RNA Meeting 2012


Anton Petrov

October 20, 2012


  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
  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
  9. None
  10. Representative structure

  11. Exploring your favorite structure

  12. None
  13. Basepair interactions

  14. RNA 3D motifs found in this structure

  15. Instances of a recurrent RNA 3D motif from the Motif

  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

  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

  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. 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