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Comparative Modeling of RNA 3D structures with ModeRNA Magdalena Musielak & Kristian Rother LABORATORY OF STRUCTURAL BIOINFORMATICS, UAM POZNAN
ModeRNA: Comparative modeling
ModeRNA: Comparative Modeling TEMPLATE ... ... TARGET Copying residues Exchanging bases Removing modifications Adding modifications Inserting loops Details: Poster W44 iimcb.genesilico.pl/moderna
ModeRNA: Results We generated 7220 models of tRNAs with known 3D structure (99 templates * 98) MODEL of 1QF6 iimcb.genesilico.pl/moderna ORIGINAL STRUCTURE
Implementation Python, Bio.PDB, PyCogent Development process – 1st wrote prototype – 2nd designed class structure (partially UML) – 3rd Test Driven Development (303 tests) Release every 3 months → Users! CLI + facade class + API → Documentation! iimcb.genesilico.pl/moderna
Pair Programming: Clear responsibilities in your team
Future Plans ModeRNA is GPL: iimcb.genesilico.pl/moderna Future Plans Combine functions for analyzing base pairs, stacking, etc. in a single software library. Utilize this information to improve 3D modeling Build more models Integrate with the big Python libraries. iimcb.genesilico.pl/moderna
Acknowledgements Magdalena Musielak Tomasz Puton Ania Czerwoniec Natalia Szostak Piotr Byzia Lukasz Koscinski Janusz M. Bujnicki BioPython & PyCogent Thomas Hamelryck Sandra Smit Rob Knight
ModeRNA: Results iimcb.genesilico.pl/moderna

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Rother_ModeRNA_BOSC2009

  • 1. Comparative Modeling of RNA 3D structures with ModeRNA Magdalena Musielak & Kristian Rother LABORATORY OF STRUCTURAL BIOINFORMATICS, UAM POZNAN
  • 3. ModeRNA: Comparative Modeling TEMPLATE ... ... TARGET Copying residues Exchanging bases Removing modifications Adding modifications Inserting loops Details: Poster W44 iimcb.genesilico.pl/moderna
  • 4. ModeRNA: Results We generated 7220 models of tRNAs with known 3D structure (99 templates * 98) MODEL of 1QF6 iimcb.genesilico.pl/moderna ORIGINAL STRUCTURE
  • 5. Implementation Python, Bio.PDB, PyCogent Development process – 1st wrote prototype – 2nd designed class structure (partially UML) – 3rd Test Driven Development (303 tests) Release every 3 months → Users! CLI + facade class + API → Documentation! iimcb.genesilico.pl/moderna
  • 6.
  • 8. Future Plans ModeRNA is GPL: iimcb.genesilico.pl/moderna Future Plans Combine functions for analyzing base pairs, stacking, etc. in a single software library. Utilize this information to improve 3D modeling Build more models Integrate with the big Python libraries. iimcb.genesilico.pl/moderna
  • 9. Acknowledgements Magdalena Musielak Tomasz Puton Ania Czerwoniec Natalia Szostak Piotr Byzia Lukasz Koscinski Janusz M. Bujnicki BioPython & PyCogent Thomas Hamelryck Sandra Smit Rob Knight
  • 10. ModeRNA: Results iimcb.genesilico.pl/moderna