1. Liron Barzilay and Tom Susel Project Advisor: Prof. Ruth Nussinov Faculty of Life Sciences, Computer Science Department Bar-Ilan University Nussinov-Wolfson Structural Bioinformatics Group, Faculty of Exact Sciences Tel Aviv University

3. Bacteriophage MS2 CapsidHepatitis delta virus Ribozyme E. Coli Initiator tRNA receptor 3 ectodomain complex with double-stranded RNA Haloarcula marismortui 50s ribosomal unit

5. Shallow groove Deep groove

6.  ?

7.  >50% of all ncRNA nucleotides  Most conserved (even more than loops)  Usually Small (<15 BP, Common 2 BP)  1D≈2D

8.  ~800 ncRNAs.  ~14500 Helixes.  ~125000 2-BP Helixes (Window 2).

9.  mRNAs: 4-Letter Language.  ncRNAs: ~110-Letter Language.  mRNAs: Standard 3’-5’/5’-3’.  ncRNAs: ~3% Reversed 3’-5’/3’-5’.

10.  mRNAs: Non-WC BPs Are Rare.  ncRNAs: ~40% Non-WC BPs.  mRNAs: Complete Phosphate Skeleton.  ncRNAs: ~80% Have One or More Phosphate Missing. 

11. Strand AStrand BPositions APositions B Manual selection of ncRNA find_pairs Initial DB Only Valid Helixes BP Manager

12. Strand AStrand BPositions APositions B Distance Matrix Engine All Against All RMSD 9240X92406848X6848 2273X2273

13. Levenshtein Distance (Edit Distance) Inner Cluster RMSD (for closest members)

15. C++: ~2200 lines. Perl: ~1200 lines. Html/Java script: ~200 lines. Memory and Multi-Processing Optimized. Include Wrap for 3 external tools. BP Manager: 2 hours.  500mb of Helix-Only PDBs DM Engine:8h x 5 = 40 hours. Perl Scripts:30m x 5 = 2.5 hours. C++ code is for Ubuntu (Multi- Processing). Perl is OS-Independent. DM Engine and the associated Perl scripts are very demanding. For window 2 we needed Quad Core @ 3.0 GHz with 4gb of Memory to complete the run before memory overload. Started with 1.2gb of ncRNA PDBs 305mb of small PDBs + 2.2gb of Matrices