1. How does the genome of an organism
Modelling proteomes
Ram Samudrala
University of Washington
How does the genome of an organism
specify its behaviour
and characteristics?

2. Proteome – all proteins of a particular system
~60,000 in human
~60,000 in rice
~4500 in bacteria
like Salmonella and
E. coli
Several thousand
distinct sequence
families

3. Modelling proteomes – understand the structure of individual proteins
A few thousand
distinct structural
folds

4. Modelling proteomes – understand their individual functions
Thousands of
possible functions

5. Modelling proteomes – understand their expression
Different expression
patterns based on
time and location

6. Modelling proteomes – understand their interactions
Interactions and
expression patterns
are interdependent
with structure and
function

7. CASP6 prediction (model1) for T0281 4.3 Å Cα RMSD for all 70 residues
Sheets –no copying- pairing and packing
Ling-Hong Hung/Shing-Chung Ngan

8. CASP6 prediction (model1) for T0271
2.4 Å Cα RMSD for all 142 residues (46% ID)
Tianyun Liu

9. Function prediction from structure
Kai Wang

10. E. coli predicted protein interaction network
Jason McDermott

11. M. tuberculosis predicted protein interaction network
Jason McDermott

12. C. elegans predicted protein interaction network
Jason McDermott

13. H. sapiens predicted protein interaction network
Jason McDermott

14. Bioverse – v2.0
Michal Guerquin/Zach Frazier

15. Bioverse - Integrator
Aaron Chang

16. + + Computational Functional Structural biology genomics genomics
Where is all this going?
Computational
biology +
Structural
genomics
Functional
genomics +
Take home message
Prediction of protein structure, function, and
networks may be used to model whole genomes to
understand organismal function and evolution

17. Current group members: Past group members:
Acknowledgements
Andrew Nichols
Baishali Chanda
Chuck Mader
David Nickle
Duangdao Wichadakul
Duncan Milburn
Ersin Emre Oren
Ekachai Jenwitheesuk
Gong Cheng
Jason McDermott
Jeremy Horst
Kai Wang
Ling-Hong Hung
Michal Guerquin
Sarunya Suebtragoon
Shing-Chung Ngan
Stewart Moughon
Tianyun Liu
Weerayuth Kittichotirat
Zach Frazier
Lisa Anichini, Program Manager
Current group members:
Aaron Chang
Marissa LaMadrid
Mike Inouye
Past group members:
Funding agencies:
National Institutes of Health
National Science Foundation
Searle Scholars Program
Puget Sound Partners in Global Health
UW Advanced Technology Initiative