Exploring protein energy landscapes with hierarchical clustering

International Journal of Quantum Chemistry

Volumn 105, Issue 6, 2005, Pages 826-830

  Gront, Dominik ^a,b   Hansmann, Ulrich H E ^b   Kolinski, Andrzej ^a  

^a UNIVERSITY OF WARSAW   (Poland)

^b MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Energy landscape; Hierarchical clustering; Homology modeling; Monte Carlo sampling; Protein folding; Protein lattice model

Indexed keywords

COMPUTER SIMULATION; HIERARCHICAL SYSTEMS; MATHEMATICAL MODELS; MONTE CARLO METHODS; SAMPLING;

ENERGY LANDSCAPE; HIERARCHICAL CLUSTERING; HOMOLOGY MODELING; MONTE CARLO SAMPLING; PROTEIN FOLDING; PROTEIN LATTICE MODEL;

PROTEINS;

EID: 30544448408     PISSN: 00207608     EISSN: None     Source Type: Journal    
DOI: 10.1002/qua.20741     Document Type: Conference Paper

References (15)

1. Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S. Protein Sci 1995, 4, 561.
2. Kolinski, A.; Skolnick, J. Polymer 2004, 45, 511.
3. Kolinski, A. Acta Biochim Poloni 2004, 51, 349.
4. Kolinski, A.; Bujnicki, J. M. Proteins 2005 (in press).
5. Shortle, D.; Simons, K. T.; Baker, D. Proc Natl Acad Sci USA 1998, 95, 11158.
6. Tsai, J.; Bonneau, R.; Morozov, A. V.; Kuhlman, B.; Rohl, C. A.; Baker, D. Proteins 2003, 53, 76.
7. Park, B.; Levitt, M. J Mol Biol 1996, 258, 367.
8. Gront, D.; Kolinski, A. Bioinformatics 2005, 21, 3179.
9. Hukushima, K.; Nemoto, K. J Phys Soc Jpn 1996, 65, 1604.
10. Geyer, G. J Stat Sci 1992, 7, 473.
11. Gront, D.; Kolinski, A.; Skolnick, J. J Chem Phys 2000, 113, 5065.
12. Jain, A. K.; Murty, M. N.; Flynn, P. J. ACM Comput Surv 1999, 31, 264.
13. Betancourt, M. R.; Skolnick, J. J Comp Chem 2001, 22, 339.
14. Rathore, N.; Chopra, M.; de Pablo, J. J. J Comp Chem 2005, 122, 1.
15. Sippl, M. J. Proteins 1993, 17, 355.