Conformational sampling of flexible ligand-binding protein loops

Bulletin of the Korean Chemical Society

Volumn 33, Issue 3, 2012, Pages 770-774

  Lee, Gyu Rie ^a   Shin, Woong Hee ^a   Park, Hahnbeom ^a   Shin, Seokmin ^a   Seok, Chaok ^a  

^a Seoul National University   (South Korea)

Author keywords

Conformational change; Conformational sampling; Ligand binding; Loop modeling

Indexed keywords

BIOLOGICAL FUNCTIONS; CONFORMATIONAL CHANGE; CONFORMATIONAL SPACE ANNEALING; GLOBAL ENERGY; LIGAND BINDING; LIGAND-BINDING PROTEINS; LIGAND-FREE STRUCTURES; LOOP CLOSURE ALGORITHMS; LOOP CONFORMATION; LOOP STRUCTURE; MODELING METHOD; MODELING PROCESS; PROTEIN FUNCTIONS; PROTEIN-LIGAND DOCKING;

BINDING ENERGY; CONFORMATIONS; CRYSTAL STRUCTURE;

LIGANDS;

EID: 84863338907     PISSN: 02532964     EISSN: 12295949     Source Type: Journal    
DOI: 10.5012/bkcs.2012.33.3.770     Document Type: Article

References (29)

1. Rohl, C. A.; Strauss, C. E.; Chivian, D.; Baker, D. Proteins 2004, 55, 656.
2. Soto, C. S.; Fasnacht, M.; Zhu, J.; Forrest, L.; Honig, B. Proteins. 2008, 70, 834.
3. Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A. Proteins 2006, 65, 438.
4. Lee, J.; Lee, D.; Park, H.; Coutsias, E. A.; Seok, C. Proteins 2010, 78, 3428.
5. Fiser, A.; Do, R. K.; Sali, A. Protein Science: A Publication of the Protein Society 2000, 9, 1753.
6. Martí-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sánchez, R.; Melo, F.; Sali, A. Annual Review of Biophysics and Biomolecular Structure 2000, 29, 291.
7. Fernandez-Fuentes, N.; Zhai, J.; Fiser, A. Nucleic Acids Research 2006, 34, W173.
8. Fernandez-Fuentes, N.; Oliva, B.; Fiser, A. Nucleic Acids Research 2006, 34, 2085.
9. Daga, P. R.; Patel, R. Y.; Doerksen, R. J. Current Topics in Medicinal Chemistry 2010, 10, 84.
10. Taylor, J. C.; Takusagawa, F.; Markham, G. D. Biochemistry 2002, 41, 9358.
11. Murre, C.; McCaw, P. S.; Vaessin, H.; Caudy, M.; Jan, L. Y.; Jan, Y. N.; Cabrera, C. V.; Buskin, J. N.; Hauschka, S. D.; Lassar, A. B. et al. Cell 1989, 58, 537.
12. Auffinger, P.; Bielecki, L.; Westhof, E. Chemistry & Biology 2003, 10, 551.
13. Weliky, D. P.; Bennett, A. E.; Zvi, A.; Anglister, J.; Steinbach, P. J.; Tycko, R. Nature Structural Biology 1999, 6, 141.
14. Mendieta, J.; Ramírez, G.; Gago, F. Proteins 2001, 44, 460.
15. Ragona, L.; Fogolari, F.; Catalano, M.; Ugolini, R.; Zetta, L.; Molinari, H. The Journal of Biological Chemistry 2003, 278, 38840.
16. Carlson, H. A.; McCammon, J. A. Molecular Pharmacology 2000, 57, 213.
17. Teague, S. J. Nature Reviews Drug Discovery 2003, 2, 527.
18. Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Journal of the American Chemical Society 2005, 127, 9632.
19. Guallar, V.; Jacobson, M.; McDermott, A.; Friesner, R. A. Journal of Molecular Biology 2004, 337, 227.
20. Shehu, A.; Clementi, C.; Kavraki, L. E. Proteins 2006, 65, 164.
21. Murphy, P. M.; Bolduc, J. M.; Gallaher, J. L.; Stoddard, B. L.; Baker, D. Proceedings of the National Academy of Sciences of the United States of America 2009, 106, 9215.
22. Park, H.; Seok, C. in revision. (Modeling of Unreliable Local Regions in Template-based Protein Models)
23. Lee, J.; Scheraga, H. A.; Rackovsky, S. Journal of Computational Chemistry 1997, 18, 1222.
24. Coutsias, E. A.; Seok, C.; Jacobson, M. P.; Dill, K. A. Journal of Computational Chemistry 2004, 25, 510.
25. Wong, S.; Jacobson, M. P. Proteins 2008, 71, 153.
26. Yang, Y.; Zhou, Y. Proteins 2008, 72, 793.
27. Zhao, S.; Zhu, K.; Li, J.; Friesner, R. A. 2011, in press.
28. Zhao, Y.; Sanner, M. F. Proteins 2007, 68, 726.
29. Wong, C. F.; Kua, J.; Zhang, Y.; Straatsma, T. P.; McCammon, J. A. Proteins 2005, 61, 850.