Modeling molecular kinetics with tICA and the kernel trick

Journal of Chemical Theory and Computation

Volumn 11, Issue 2, 2015, Pages 600-608

  Schwantes, Christian R ^a   Pande, Vijay S ^a,b  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIPEPTIDE;

CHEMISTRY; KINETICS; MOLECULAR DYNAMICS; MOLECULAR MODEL; STATISTICAL MODEL; TIME FACTOR;

DIPEPTIDES; KINETICS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR DYNAMICS SIMULATION; TIME FACTORS;

EID: 84922674715     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct5007357     Document Type: Article

References (50)

1. Levitt, M. Nat. Struct. Mol. Biol. 2001, 8, 392-393
2. Karplus, M.; McCammon, J. A. Nat. Struct. Mol. Biol. 2002, 9, 646-652
3. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. Science 2011, 334, 517-520
4. Lane, T. J.; Bowman, G. R.; Beauchamp, K.; Voelz, V. A.; Pande, V. S. J. Am. Chem. Soc. 2011, 133, 18413-18419
5. Voelz, V. A.; Jäger, M.; Yao, S.; Chen, Y.; Zhu, L.; Waldauer, S. A.; Bowman, G. R.; Friedrichs, M.; Bakajin, O.; Lapidus, L. J.; Weiss, S.; Pande, V. S. J. Am. Chem. Soc. 2012, 134, 12565-12577
6. Buch, I.; Giorgino, T.; De Fabritiis, G. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 10184-10189
7. Shan, Y.; Kim, E. T.; Eastwood, M. P.; Dror, R. O.; Seeliger, M. A.; Shaw, D. E. J. Am. Chem. Soc. 2011, 133, 9181-9183
8. Dror, R. O.; Pan, A. C.; Arlow, D. H.; Borhani, D. W.; Maragakis, P.; Shan, Y.; Xu, H.; Shaw, D. E. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 13118-13123
9. Ivetac, A.; McCammon, J. A. J. Mol. Biol. 2009, 388, 644-658
10. Ostmeyer, J.; Chakrapani, S.; Pan, A. C.; Perozo, E.; Roux, B. Nature 2013, 121-124
11. Lin, Y.-L.; Meng, Y.; Jiang, W.; Roux, B. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 1664-1669
12. Shukla, D.; Meng, Y.; Roux, B.; Pande, V. S. Nat. Commun. 2014, 5, 3397
13. Kohlhoff, K. J.; Shukla, D.; Lawrenz, M.; Bowman, G. R.; Konerding, D. E.; Belov, D.; Altman, R. B.; Pande, V. S. Nat. Chem. 2014, 6, 15-21
14. Shirts, M.; Pande, V. S. Science 2000, 290, 1903-1904
15. Shaw, D. E.; Deneroff, M. M.; Dror, R. O.; Kuskin, J. S.; Larson, R. H.; Salmon, J. K.; Young, C.; Batson, B.; Bowers, K. J.; Chao, J. C.; Eastwood, M. P.; Gagliardo, J.; Grossman, J. P.; Ho, C. R.; Ierardi, D. J.; Kolossváry, I.; Klepeis, J. L.; Layman, T.; McLeavey, C.; Moraes, M. A.; Mueller, R.; Priest, E. C.; Shan, Y.; Spengler, J.; Theobald, M.; Towles, B.; Wang, S. C. Commun. ACM 2008, 51, 91-97
16. Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. J. Comput. Chem. 2009, 30, 864-872
17. Buch, I.; Harvey, M. J.; Giorgino, T.; Anderson, D. P.; De Fabritiis, G. J. Chem. Inf. Model. 2010, 50, 397-403
18. Eastman, P.; Friedrichs, M. S.; Chodera, J. D.; Radmer, R. J.; Bruns, C. M.; Ku, J. P.; Beauchamp, K. A.; Lane, T. J.; Wang, L.-P.; Shukla, D.; Tye, T.; Houston, M.; Stich, T.; Klein, C.; Shirts, M. R.; Pande, V. S. J. Chem. Theory Comput. 2013, 9, 461-469
19. Götz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. J. Chem. Theory Comput. 2012, 8, 1542-1555
20. Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. Bioinformatics 2013, 29, 845-854
21. Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. Curr. Opin. Struct. Biol. 2013, 23, 58-65
22. Schwantes, C. R.; Pande, V. S. J. Chem. Theory Comput. 2013, 9, 2000-2009
23. Silva, D.-A.; Weiss, D. R.; Avila, F. P.; Da, L.-T.; Levitt, M.; Wang, D.; Huang, X. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 7665-7670
24. Bowman, G. R.; Geissler, P. L. J. Phys. Chem. B 2014, 118, 6417-6423
25. Prinz, J.-H.; Wu, H.; Sarich, M.; Keller, B.; Senne, M.; Held, M.; Chodera, J. D.; Schütte, C.; Noé, F. J. Chem. Phys. 2011, 134, 174105
26. Beauchamp, K. A.; Bowman, G. R.; Lane, T. J.; Maibaum, L.; Haque, I. S.; Pande, V. S. J. Chem. Theory Comput. 2011, 7, 3412-3419
27. McGibbon, R. T.; Schwantes, C. R.; Pande, V. S. J. Phys. Chem. B 2014, 118, 6475-6481
28. Pérez-Hernández, G.; Paul, F.; Giorgino, T.; De Fabritiis, G.; Noé, F. J. Chem. Phys. 2013, 139, 015102
29. McGibbon, R. T.; Pande, V. S. J. Chem. Theory Comput. 2013, 9, 2900-2906
30. Zhou, T.; Caflisch, A. J. Chem. Theory Comput. 2012, 8, 2930-2937
31. Kellogg, E. H.; Lange, O. F.; Baker, D. J. Phys. Chem. B 2012, 116, 11405-11413
32. Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y.; Wriggers, W. Science 2010, 330, 341-346
33. Schütte, C.; Huisinga, W.; Deuflhard, P. Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems; Springer: New York, 2001; pp 191-223.
34. Noé, F.; Nüske, F. Multiscale Model. Simul. 2013, 11, 635-655
35. Nüske, F.; Keller, B. G.; Pérez-Hernández, G.; Mey, A. S.; Noé, F. J. Chem. Theory Comput. 2014, 10, 1739-1752
36. Molgedey, L.; Schuster, H. Phys. Rev. Lett. 1994, 72, 3634-3637
37. Blaschke, T.; Berkes, P.; Wiskott, L. Neural Comput. 2006, 18, 2495-2508
38. Naritomi, Y.; Fuchigami, S. J. Chem. Phys. 2011, 134, 065101
39. Schölkopf, B.; Smola, A.; Müller, K.-R. Neural Comput. 1998, 10, 1299-1319
40. Schölkopf, B.; Smola, A.; Müller, K.-R. In Artificial Neural Networks-ICANN'97; Gerstner, W.; Germond, A.; Hasler, M.; Nicoud, J.-D., Eds.; Lecture Notes in Computer Science; Springer: Berlin, Heidelberg, 1997; Vol. 1327; pp 583-588.
41. Mika, S.; Ratsch, G.; Weston, J.; Schölkopf, B.; Müller, K. In Neural Networks for Signal Processing IX, 1999. Proceedings of the 1999 IEEE Signal Processing Society Workshop, Madison, WI, Aug. 23-25, 1999; pp 41 - 48.
42. Fukumizu, K.; Bach, F. R.; Gretton, A. J. Mach. Learn. Res. 2007, 8, 361-383
43. Bach, F. R.; Jordan, M. I. J. Mach. Learn. Res. 2003, 3, 1-48
44. Cortes, C.; Vapnik, V. Mach. Learn. 1995, 20, 273-297
45. Williams, C.; Seeger, M. In Proceedings of the 14th Annual Conference on Neural Information Processing Systems, 2001; pp 682 - 688.
46. Smola, A. J.; Schölkopf, B. In Proceedings of the Seventeenth International Conference on Machine Learning (ICML 2000); Morgan Kaufmann: Burlington, MA, 2000; pp 911-918.
47. Müller, K.; Brown, L. D. Theor. Chim. Acta 1979, 53, 75-93
48. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Proteins Struct. Funct. Bioinf. 2010, 78, 1950-1958
49. Lapidus, L. J.; Acharya, S.; Schwantes, C. R.; Wu, L.; Shukla, D.; King, M.; DeCamp, S. J.; Pande, V. S. Biophys. J. 2014, 107, 947-955
50. Razavi, A. M.; Wuest, W. M.; Voelz, V. A. J. Chem. Inf. Model. 2014, 54, 1425-1432