Mathematical Modeling and Optimization Methods for De Novo Protein Design - Systems Biology: Networks, Models, and Applications - page 59

on algorithmic improvement on the novel de novo protein design
framework to enhance computational efficiency [82], trial and incor-
poration of non-energy-based formulations to increase accuracy of
predictions, and application of the framework on more protein targets.

ACKNOWLEDGMENTS

C.A.F. gratefully acknowledges financial support from the National Science
Foundation and the National Institutes of Health (R24 GM069736).

REFERENCES

1. Drexler, K. E. Molecular engineering: an approach to the development of

general capabilities for molecular manipulation. Proceedings of the National
Academy of Sciences USA , 78:5275-8, 1981.

2. Pabo, C. Molecular technology. Designing proteins and peptides. Nature ,

301:200, 1983.

3. Hardin, C., T. V. Pogorelov and Z. Luthey-Schulten. Ab initio protein struc-

ture prediction. Current Opinion in Structural Biology , 12:176-81, 2002.

4. Ponder, J. W. and F. M. Richards. Tertiary templates for proteins. Journal of

Molecular Biology , 193:775-91, 1987.

5. Hellinga, H. W. and F. M. Richards. Construction of new ligand binding

sites in proteins of known structure. I. Computer aided modeling of
sites with predefined geometry. Journal of Molecular Biology , 222:763-85,
1991.

6. Desjarlais, J. R. and T. M. Handel. De novo design of the hydrophobic cores

of proteins. Protein Science , 4:2006-18, 1995.

7. Dahiyat, B. I. and S. L. Mayo. Protein design automation. Protein Science ,

5:895-903, 1996.

8. Dahiyat, B. I., D. B. Gordon and S. L. Mayo. Automated design of the sur-

face positions of protein helices. Protein Science , 6:1333-7, 1997.

9. Raha, K., A. M. Wollacott, M. J. Italia and J. R. Desjarlais. Prediction of

amino acid sequence from structure. Protein Science , 9:1106-19, 2000.

10. Street, A. G. and S. L. Mayo. Pairwise calculation of protein solvent-accessible

surface areas. Folding and Design , 3:253-8, 1998.

11. Nohaile, M. J., Z. S. Hendsch, B. Tidor and R. T. Sauer. Altering dimeriza-

tion specificity by changes in surface electrostatics. Proceedings of the
National Academy of Sciences USA , 98:3109-14, 2001.

12. Koehl, P. and M. Levitt. De novo protein design. I. In search of stability and

specificity. Journal of Molecular Biology , 293:1161-81, 1999.

13. Wernisch, L., S. Hery and S. J. Wodak. Automatic protein design with all

atom force-fields by exact and heuristic optimization. Journal of Molecular
Biology , 301:713-36, 2000.

14. Lim, W. A., A. Hodel, R. T. Sauer and F. M. Richards. Crystal structure of a

mutant protein with altered but improved hydrophobic core packing.
Proceedings of the National Academy of Sciences USA , 91:423-7, 1994.