Identifying and reducing error in cluster-expansion approximations of protein energies

Journal of Computational Chemistry

Volumn 31, Issue 16, 2010, Pages 2900-2914

  Hahn, Seungsoo ^a   Ashenberg, Orr ^a   Grigoryan, Gevorg ^b   Keating, Amy E ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Cluster expansion; Energy function; Heterogeneous variance; Protein design; Protein modeling

Indexed keywords

DESIGN; DIMERS; ECONOMIC AND SOCIAL EFFECTS; FUNCTION EVALUATION; ITERATIVE METHODS; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; SOFTWARE ENGINEERING;

CLUSTER EXPANSION; ENERGY FUNCTIONS; HETEROGENEOUS VARIANCE; PROTEIN DESIGN; PROTEIN MODELING;

PROTEINS;

LYSOZYME; PROTEIN;

ARTICLE; BACTERIOPHAGE T4; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; PROTEIN TERTIARY STRUCTURE;

BACTERIOPHAGE T4; MODELS, CHEMICAL; MODELS, MOLECULAR; MURAMIDASE; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 79952117766     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21585     Document Type: Article

References (36)

1. Harbury, P. B.; Plecs, J. J.; Tidor, B.; Alber, T.; Kim, P. S. Science 1998, 282, 1462.
2. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82.
3. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Science 2003, 302, 1364.
4. Boas, F. E.; Harbury, P. B. Curr Opin Struct Biol 2007, 17, 199.
5. Ngan, S. C.; Hung, L. H.; Liu, T.; Samudrala, R. Methods Mol Biol 2008, 413, 243.
6. Lazaridis, T.; Karplus, M. Curr Opin Struct Biol 2000, 10, 139.
7. Jorgensen, W. L.; Tirado-Rives, J. Proc Natl Acad Sci USA 2005, 102, 6665.
8. Mohanty, D.; Dominy, B. N.; Kolinski, A.; Brooks, C. L., III; Skolnick, J. Proteins 1999, 35, 447.
9. Grigoryan, G.; Zhou, F.; Lustig, S. R.; Ceder, G.; Morgan, D.; Keating, A. E. PLoS Comput Biol 2006, 2, e63.
10. Zhou, F.; Grigoryan, G.; Lustig, S. R.; Keating, A. E.; Ceder, G.; Morgan, D. Phys Rev Lett 2005, 95, 148103.
11. Apgar, J. R.; Hahn, S.; Grigoryan, G.; Keating, A. E. J Comput Chem 2009, 30, 2402.
12. Grigoryan, G.; Reinke, A. W.; Keating, A. E. Nature 2009, 458, 859.
13. Harbury, P. B.; Tidor, B.; Kim, P. S. Proc Natl Acad Sci USA 1995, 92, 8408.
14. Crick, F. H. C. Acta Crystallogr 1953, 6, 685.
15. Crick, F. H. C. Acta Crystallogr 1953, 6, 689.
16. Grigoryan, G.; Keating, A. E. J Mol Biol 2006, 355, 1125.
17. Grigoryan, G.; Keating, A. E. Curr Opin Struct Biol 2008, 18, 477.
18. Lupas, A. N.; Gruber, M. Adv Protein Chem 2005, 70, 37.
19. Doyle, D. A.; Lee, A.; Lewis, J.; Kim, E.; Sheng, M.; MacKinnon, R. Cell 1996, 85, 1067.
20. Weaver, L. H.; Matthews, B. W. J Mol Biol 1987, 193, 189.
21. Landgraf, C.; Panni, S.; Montecchi-Palazzi, L.; Castagnoli, L.; Schneider-Mergener, J.; Volkmer-Engert, R.; Cesareni, G. PLoS Biol 2004, 2, E14.
22. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
23. Lazaridis, T.; Karplus, M. Proteins 1999, 35, 133.
24. Sanchez, J.; Ducastelle, F.; Gratias, D. Phys A 1984, 128, 334.
25. van de Walle, A.; Ceder, G. J Phase Equilib 2002, 23, 348.
26. Hastie, T.; Tibshirani, R.; Friedman, J. H. The Elements of Statistical Learning: Data Mining, Inference, and Prediction; Springer: New York, 2009.
27. Lane, T. P.; DuMouchel, W. H. Am Stat 1994, 48, 315.
28. Montgomery, D. C.; Peck, E. A.; Vining, G. G. Introduction to Linear Regression Analysis; Wiley: New York, 2001.
29. White, H. Econometrica 1980, 48, 817.
30. MacKinnon, J. G.; White, H. J Econ 1985, 29, 305.
31. Hung, A. Y.; Sheng, M. J Biol Chem 2002, 277, 5699.
32. Newman, J. R.; Keating, A. E. Science 2003, 300, 2097.
33. Stiffler, M. A.; Chen, J. R.; Grantcharova, V. P.; Lei, Y.; Fuchs, D.; Allen, J. E.; Zaslavskaia, L. A.; MacBeath, G. Science 2007, 317, 364.
34. Wolf-Yadlin, A.; Sevecka, M.; MacBeath, G. Curr Opin Chem Biol 2009, 13, 398.
35. Hou, T.; McLaughlin, W.; Lu, B.; Chen, K.; Wang, W. J Proteome Res 2006, 5, 32.
36. Hou, T.; Zhang, W.; Case, D. A.; Wang, W. J Mol Biol 2008, 376, 1201.