Protein inherent structures by different minimization strategies

Journal of Computational Chemistry

Volumn 32, Issue 6, 2011, Pages 1113-1116

  Rao, Francesco ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

complex networks; energy minimization; free energy surface; molecular dynamics; proteins

Indexed keywords

COMPLEX NETWORKS; DISCRETIZATIONS; ENERGY MINIMIZATION; ENERGY PROFILE; FREE-ENERGY LANDSCAPE; FREE-ENERGY SURFACE; INHERENT STRUCTURES; MICROSTATES; MOLECULAR DYNAMICS SIMULATIONS; NETWORK-BASED; OVERALL PROPERTIES; POTENTIAL ENERGY MINIMA; QUANTITATIVE AGREEMENT; QUASI-NEWTONIAN ALGORITHM;

COMPUTER SIMULATION; CONJUGATE GRADIENT METHOD; FREE ENERGY; MOLECULAR DYNAMICS; OPTIMIZATION; PEPTIDES; POTENTIAL ENERGY FUNCTIONS;

CLUSTERING ALGORITHMS;

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 79952516403     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21691     Document Type: Article

References (41)

1. Rao, F.; Caflisch, A., J Mol Biol 2004, 342, 299.
2. Krivov, S.; Karplus, M., Proc Natl Acad Sci USA 2004, 101, 14766.
3. Gfeller, D.; De Los Rios, P.; Caflisch, A.; Rao, F., Proc Natl Acad Sci USA 2007, 104, 1817.
4. Gfeller, D.; de Lachapelle, D. M.; De Los Rios, P.; Caldarelli, G.; Rao, F., Phys Rev E 2007, 76, 026113.
5. Settanni, G.; Fersht, A. R., Biophys J 2008, 94, 4444.
6. Yang, S.; Roux, B., PLoS Comput Biol 2008, 4, e1000047.
7. Prada-Gracia, D.; Gõmez-Gardeñes, J.; Echenique, P.; Falo, F., PLoS Comput Biol 2009, 5, e1000415.
8. Rao, F.; Karplus, M., Proc Natl Acad Sci USA 2010, 107, 9152.
9. Rao, F., J Phys Chem Lett 2010, 1, 1580.
10. Li, C. B.; Yang, H.; Komatsuzaki, T., Proc Natl Acad Sci USA 2008, 105, 536.
11. Ihalainen, J. A.; Bredenbeck, J.; Pfister, R.; Helbing, J.; Chi, L.; van Stokkum, I. H.; Woolley, G. A.; Hamm, P., Proc Natl Acad Sci USA 2007, 104, 5383.
12. Ihalainen, J. A.; Paoli, B.; Muff, S.; Backus, E. H.; Bredenbeck, J.; Woolley, G. A.; Caflisch, A.; Hamm, P., Proc Natl Acad Sci USA 2008, 105, 9588.
13. Swope, W.; Pitera, J.; Suits, F., J Phys Chem B 2004, 108, 6571.
14. Noé, F.; Horenko, I.; Schütte, C.; Smith, J., J Chem Phys 2007, 126, 155102.
15. Chodera, J.; Singhal, N.; Pande, V.; Dill, K.; Swope, W., J Chem Phys 2007, 125, 155101.
16. Stillinger, F.; Weber, T., Phys Rev A 1982, 25, 978.
17. Krivov, S. V.; Muff, S.; Caflisch, A.; Karplus, M., J Phys Chem B 2008, 112, 8701.
18. Strodel, B.; Wales, D., Chem Phys Lett 2008, 466, 105.
19. Evans, D.; Wales, D., J Chem Phys 2003, 119, 9947.
20. Evans, D.; Wales, D., J Chem Phys 2004, 121, 1080.
21. Khalili, M.; Wales, D., J Phys Chem B 2008, 112, 2456.
22. Czerminski, R.; Elber, R., J Chem Phys 1990, 92, 5580.
23. Berry, R. S.; Elmaci, N.; Rose, J. P.; Vekhter, B., Proc Natl Acad Sci USA 1997, 94, 9520.
24. Baumketner, A.; Shea, J.-E.; Hiwatari, Y., Phys Rev E 2003, 67, 011912.
25. Nakagawa, N.; Peyrard, M., Proc Natl Acad Sci USA 2006, 103, 5279.
26. Kim, J.; Keyes, T., J Phys Chem B 2007, 111, 2647.
27. Leach, A., Molecular Modelling: Principles and Applications; Addison-Wesley Longman Ltd, 2001.
28. Walsh, T. R.; Wales, D., Z Phys D 1997, 40, 229.
29. Chakravarty, C.; Debenedetti, P.; Stillinger, F., J Chem Phys 2005, 123, 206101.
30. Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M., J Comput Chem 1983, 4, 187.
31. Liu, D.; Nocedal, J., Math Program 1989, 45, 503.
32. Cecchini, M.; Houdusse, A.; Karplus, M., PLoS Comput Biol 2008, 4, e1000129.
33. Haberthur, U.; Caflisch, A., J Comput Chem 2008, 29, 701.
34. Bieri, O.; Wirz, J.; Hellrung, B.; Schutkowski, M.; Drewello, M.; Kiefhaber, T., Proc Natl Acad Sci USA 1999, 96, 9597.
35. Möglich, A.; Joder, K.; Kiefhaber, T., Proc Natl Acad Sci USA 2006, 103, 12394.
36. Krivov, S. V.; Karplus, M., J Phys Chem B 2006, 110, 12689.
37. Ferrara, P.; Caflisch, A., Proc Natl Acad Sci USA 2000, 97, 10780.
38. Rao, F.; Caflisch, A., J Chem Phys 2003, 119, 4035.
39. Muff, S.; Caflisch, A., J Chem Phys 2009, 130, 125104.
40. Wales, D.; Doye, J.; Miller, M.; Mortenson, P.; Walsh, T., Adv Chem Phys 2000, 115, 1.
41. Małolepsza, E.; Strodel, B.; Khalili, M.; Trygubenko, S.; Fejer, S. N.; Wales, D. J., J Comput Chem 2010, 31, 1402.