Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing

Journal of Computational Chemistry

Volumn 29, Issue 14, 2008, Pages 2479-2484

  Lee, Jinwoo ^a,b   Joo, Keehyoung ^b   Kim, Seung Yeon ^c   Lee, Jooyoung ^b  

^a Kwangwoon University   (South Korea)

^b Korea Institute for Advanced Study   (South Korea)

^c Chungju National University   (South Korea)

Author keywords

Energy landscape; Global optimization; Protein model; Structure optimization

Indexed keywords

ANNEALING; CONFORMATIONS; ELECTRIC CURRENTS; HYDROPHILICITY; MONOMERS; OPTIMIZATION; RHENIUM; STRUCTURAL DESIGN; STRUCTURAL OPTIMIZATION;

CO-ORDINATE SYSTEMS; CONFORMATIONAL SPACE ANNEALING; ENERGY LANDSCAPE; ENERGY LANDSCAPES; FIBONACCI SEQUENCES; HYDROPHILIC MONOMERS; LOW-ENERGY CONFORMATIONS; PROTEIN MODEL; QUOTIENT SPACE; SEARCH SPACES; SHIFT OPERATORS; STRUCTURE OPTIMIZATION; THREE DIMENSIONS;

GLOBAL OPTIMIZATION;

PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; THERMODYNAMICS;

MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 52649170222     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20995     Document Type: Article

References (21)

1. Anfinsen, C. B. Science 1973, 181, 223.
2. Joo, K.; Lee, J.; Lee, S.; Seo, J.; Lee, S. J.; Lee, J. Proteins 2007, 69 Suppl. 8, 83.
3. Stillinger, F. H.; Head-Gordon, T.; Hirshfeld, C. L. Phys Rev E 1993, 48, 1469.
4. Hsu, H.-P.; Mehra, V.; Nadler, W.; Grassberger, P. J Chem Phys 2003. 118, 444.
5. Liang, F. J Chem Phys 2004, 120, 6756.
6. Kim, S. Y.; Lee, S. B.; Lee, J. Phys Rev E 2005, 72, 011916.
7. Kim, J.; Straub, J. E.; Keyes, T. Phys Rev Lett 2006, 97, 050601.
8. Bachmann, M.; Arkin, H.; Janke, W. Phys Rev E 2005, 71, 031906.
9. Kim, J.; Straub, J. E.; Keyes, T. Phys Rev E 2007, 76, 011913.
10. Lee, J.; Scheraga, H, A.; Rackovsky, S. J Comput Chem 1997, 18. 1222.
11. Lee, J.; Liwo, A.; Scheraga, H. A. Proc Natl Acad Sci USA 1999, 96, 2025.
12. Lee, J.; Lee, I. H.; Lee, J. Phys Rev Lett 2003, 91, 080201.
13. Irbäck, A.; Peterson, C.; Potthast, F.; Sommelius, O. J Chem Phys 1997, 107, 273.
14. Wu, S.; Skolnick, J.; Zhang, Y. BMC Biol 2007, 5, 17.
15. Lee, J.; Pillardy, C.; Czaplewski, J.; Arnautova, Y.; Ripoll, D. R.; Liwo, A.; Gibson, K. D.; Wawak, R. J.; Scheraga, H. A., Comput Phys Commun 2000, 128, 399.
16. Lee, J.; Scheraga, H. A. Int J Quant Chem 1999, 75, 255.
17. Lee, J.; Liwo, A.; Ripoll, D.; Pillardy, J.; Saunders, J. A.; Gibson, K. D.; Scheraga, H. A. Int J Quant Chem 2000, 77, 90.
18. Zhang, Y.; Skolnick, J. Proteins 2004, 57, 702.
19. Zhang, Y. C.; Ma, J. J. Phys Rev E 2007, 76, 036708.
20. Berg, B. A.; Neuhaus, T. Phys Rev Lett 1992, 68, 9.
21. Lee, Y. J. Phys Rev Lett 1993, 71, 211.