Physically realistic homology models built with ROSETTA can be more accurate than their templates

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 14, 2006, Pages 5361-5366

  Misura, Kira M S ^a   Chivian, Dylan ^a,b   Rohl, Carol A ^a,c   Kim, David E ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c ROSETTA INPHARMATICS   (United States)

Author keywords

Fragment assembly; Structure prediction

Indexed keywords

HYDROGEN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; ATOM; CHEMICAL MODEL; COMPUTER PROGRAM; CRYSTAL STRUCTURE; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STEREOCHEMISTRY; STRUCTURE ANALYSIS;

MODELS, THEORETICAL; PROTEIN FOLDING; PROTEINS;

EID: 33645792604     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0509355103     Document Type: Article

References (23)

1. Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F. & Sali, A. (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 291-325.
2. Wallner, B. & Elofsson, A. (2005) Protein Sci. 14, 1315-1327.
3. Tramontane, A., Leplae, R. & Morea, V. (2001) Proteins, Suppl. 5, 22-38.
4. Tramontano, A. & Morea, V. (2003) Proteins 53, Suppl. 6, 352-368.
5. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993) J. Appl. Cryst. 26, 291-294.
6. Hooft, R. W., Vriend, G., Sander, C. & Abola, E. E. (1996) Nature 381, 272.
7. Lovell, S. C., Davis, I. W., Arendall, W. B., III, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S. & Richardson, D. C. (2003) Proteins 50, 437-450.
8. Rohl, C. A., Strauss, C. E., Misura, K. M. & Baker, D. (2004) Methods Enzymol. 383, 66-93.
9. Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225.
10. Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker, D. (1999) Proteins 34, 82-95.
11. Chivian, D., Kim, D. E., Malmstrom, L., Bradley, P., Robertson, T., Murphy, P., Strauss, C. E., Bonneau, R., Rohl, C. A. & Baker, D. (2003) Proteins 53, Suppl. 6, 524-533.
12. Rohl, C. A., Strauss, C. E., Chivian, D. & Baker, D. (2004) Proteins 55, 656-677.
13. Fiser, A. & Sali, A. (2003) Methods Enzymol. 374, 461-491.
14. Chothia, C. & Lesk, A. M. (1986) EMBO J. 5, 823-826.
15. Plewczynski, D., Pas, J., Von Grotthuss, M. & Rychlewski, L. (2004) Acta Biochim. Polonica 51, 161-172.
16. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
17. Misura, K. M. & Baker, D. (2005) Proteins 59, 15-29.
18. Bradley, P., Misura, K. M. & Baker, D. (2005) Science 309, 1868-1871.
19. Anderson, D. P. (2005) Berkeley Open Infrastructure fur Network Computing (BOINC) (University of California, Berkeley, CA).
20. Shortle, D., Simons, K. T. & Baker, D. (1998) Proc. Natl. Acad. Sci. USA 95, 11158-11162.
21. Kinch, L. N., Wrabl, J. O., Krishna, S. S., Majumdar, I., Sadreyev, R. I., Qi, Y., Pei, J., Cheng, H. & Grishin, N. V. (2003) Proteins 53, Suppl. 6, 395-409.
22. Bonneau, R., Strauss, C. E. M. & Baker, D. (2001) Proteins Struct. Funct. Genet. 43, 1-11.
23. DeLano, W. L. (2002) The PYMOL Molecular Graphics System (DeLano Scientific, San Carlos, CA).