Rother_ModeRNA_BOSC2009

•

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Technology Education

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

2. ModeRNA: Comparative modeling

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.

7. Pair Programming: Clear responsibilities in your team

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