SCOPUS 정보 검색 플랫폼

Journal of Chemical Physics

Volumn 135, Issue 22, 2011, Pages

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

(2) Spiwok, Vojětch a,b Králová, Blanka a

a INSTITUTE OF CHEMICAL TECHNOLOGY (Czech Republic)

b INSTITUTE OF CHEMISTRY (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

3-D SPACE; ATOMIC MOTION; BIAS POTENTIAL; COLLECTIVE MOTIONS; COLLECTIVE VARIABLES; CONFORMATIONAL FREE ENERGY; CONFORMATIONAL SPACE; DIMENSIONALITY REDUCTION; EMBEDDINGS; GENERAL PURPOSE; METADYNAMICS; NONLINEAR DIMENSIONALITY REDUCTION; SIMULATION TECHNIQUE; THREE DIMENSIONS; TRANSITION STRUCTURES;

BOATS; FREE ENERGY; NONLINEAR ANALYSIS; THREE DIMENSIONAL;

CONFORMATIONS;

ALGORITHM; ARTICLE; CONFORMATION; MOLECULAR DYNAMICS; MOTION; NONLINEAR SYSTEM; THERMODYNAMICS;

ALGORITHMS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MOTION; NONLINEAR DYNAMICS; THERMODYNAMICS;

EID: 83755206813 PISSN: 00219606 EISSN: None Source Type: Journal
DOI: 10.1063/1.3660208 Document Type: Article

Times cited : (65)

References (40)

1
- 0042797442
- (Cambridge University Press, Cambridge, UK)
- D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, UK, 2003).
- (2003) Energy Landscapes
- Wales, D.J.¹

2
- 0036286654
- 10.1021/ar010030m
- T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 35, 430 (2002). 10.1021/ar010030m
- (2002) Acc. Chem. Res. , vol.35 , pp. 430
- Simonson, T.¹ Archontis, G.² Karplus, M.³

3
- 32344450229
- Network and graph analyses of folding free energy surfaces
- DOI 10.1016/j.sbi.2006.01.002, PII S0959440X06000029
- A. Caflisch, Curr. Opin. Struct. Biol. 16, 71 (2006). 10.1016/j.sbi.2006.01.002 (Pubitemid 43221874)
- (2006) Current Opinion in Structural Biology , vol.16 , Issue.1 , pp. 71-78
- Caflisch, A.¹

4
- 0036790894
- 10.1073/pnas.202427399
- A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 1256 (2002). 10.1073/pnas.202427399
- (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 1256
- Laio, A.¹ Parrinello, M.²

5
- 0041810451
- 10.1103/PhysRevLett.90.238302
- M. Iannuzzi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 90, 238302 (2003). 10.1103/PhysRevLett.90.238302
- (2003) Phys. Rev. Lett. , vol.90 , pp. 238302
- Iannuzzi, M.¹ Laio, A.² Parrinello, M.³

6
- 58149299971
- 10.1088/0034-4885/71/12/126601
- A. Laio and F. L. Gervasio, Rep. Prog. Phys. 71, 126601 (2008). 10.1088/0034-4885/71/12/126601
- (2008) Rep. Prog. Phys. , vol.71 , pp. 126601
- Laio, A.¹ Gervasio, F.L.²

7
- 84875760613
- 10.1002/wcms.31
- A. Barducci, M. Bonomi, and M. Parrinello, WIREs Comput. Mol. Sci. 1, 826 (2011). 10.1002/wcms.31
- (2011) WIREs Comput. Mol. Sci. , vol.1 , pp. 826
- Barducci, A.¹ Bonomi, M.² Parrinello, M.³

8
- 77951585445
- 10.1021/jp100950w
- J. Vymtal and J. Vondrek, J. Phys. Chem. B 114, 5632 (2010). 10.1021/jp100950w
- (2010) J. Phys. Chem. B , vol.114 , pp. 5632
- Vymtal, J.¹ Vondrek, J.²

9
- 34848879539
- The conformational free energy landscape of β-D-glucopyranose. Implications for substrate preactivation in β-glucoside hydrolases
- DOI 10.1021/ja068411o
- X. Biarnés, A. Ardvol, A. Planas, C. Rovira, A. Laio, and M. Parrinello, J. Am. Chem. Soc. 129, 10686 (2007). 10.1021/ja068411o (Pubitemid 350067477)
- (2007) Journal of the American Chemical Society , vol.129 , Issue.35 , pp. 10686-10693
- Biarnes, X.¹ Ardevol, A.² Planas, A.³ Rovira, C.⁴ Laio, A.⁵ Parrinello, M.⁶

10
- 69949115243
- 10.1080/08927020802647280
- D. Quigley and P. M. Rodger, Mol. Simul. 35, 613 (2009). 10.1080/08927020802647280
- (2009) Mol. Simul. , vol.35 , pp. 613
- Quigley, D.¹ Rodger, P.M.²

11
- 29244487921
- 3 post-perovskite phase
- DOI 10.1038/nature04439
- A. R. Oganov, R. Martok, A. Laio, P. Raiteri, and M. Parrinello, Nature (London) 438, 1142 (2005). 10.1038/nature04439 (Pubitemid 41831681)
- (2005) Nature , vol.438 , Issue.7071 , pp. 1142-1144
- Oganov, A.R.¹ Martonak, R.² Laio, A.³ Raiteri, P.⁴ Parrinello, M.⁵

12
- 73349098763
- 10.1021/ct900202f
- F. Pietrucci, and A. Laio, J. Chem. Theor. Comput. 5, 2197 (2009). 10.1021/ct900202f
- (2009) J. Chem. Theor. Comput. , vol.5 , pp. 2197
- Pietrucci, F.¹ Laio, A.²

13
- 0027441950
- Essential dynamics of proteins
- DOI 10.1002/prot.340170408
- A. Amadei, A. B. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993). 10.1002/prot.340170408 (Pubitemid 23358549)
- (1993) Proteins: Structure, Function and Genetics , vol.17 , Issue.4 , pp. 412-425
- Amadei, A.¹ Linssen, A.B.M.² Berendsen, H.J.C.³

14
- 34147097967
- Metadynamics in essential coordinates: Free energy simulation of conformational changes
- DOI 10.1021/jp068587c
- V. Spiwok, P. Lipovov, and B. Krlov, J. Phys. Chem. B 111, 3073 (2007). 10.1021/jp068587c (Pubitemid 46573451)
- (2007) Journal of Physical Chemistry B , vol.111 , Issue.12 , pp. 3073-3076
- Spiwok, V.¹ Lipovova, P.² Kralova, B.³

15
- 53149099307
- 10.1007/s00894-008-0343-7
- V. Spiwok, B. Krlov, and I. Tvaroka, J. Mol. Model. 14, 995 (2008). 10.1007/s00894-008-0343-7
- (2008) J. Mol. Model. , vol.14 , pp. 995
- Spiwok, V.¹ Krlov, B.² Tvaroka, I.³

16
- 78651327755
- 10.1021/ct100413b
- L. Sutto, M. D'Abramo, and F. L. Gervasio, J. Chem. Theory Comput. 6, 3640 (2010). 10.1021/ct100413b
- (2010) J. Chem. Theory Comput. , vol.6 , pp. 3640
- Sutto, L.¹ D'Abramo, M.² Gervasio, F.L.³

17
- 0034704229
- A global geometric framework for nonlinear dimensionality reduction
- DOI 10.1126/science.290.5500.2319
- J. B. Tenenbaum, V. de Silva, and J. C. Langford, Science 290, 2319 (2000). 10.1126/science.290.5500.2319 (Pubitemid 32041577)
- (2000) Science , vol.290 , Issue.5500 , pp. 2319-2323
- Tenenbaum, J.B.¹ De Silva, V.² Langford, J.C.³

18
- 33745611125
- Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
- DOI 10.1073/pnas.0603553103
- P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi, Proc. Natl. Acad. Sci. U.S.A. 103, 9885 (2006). 10.1073/pnas.0603553103 (Pubitemid 43993592)
- (2006) Proceedings of the National Academy of Sciences of the United States of America , vol.103 , Issue.26 , pp. 9885-9890
- Das, P.¹ Moll, M.² Stamati, H.³ Kavraki, L.E.⁴ Clementi, C.⁵

19
- 77956391259
- 10.1073/pnas.1003293107
- A. L. Ferguson, A. Z. Panagiotopoulos, P. G. Debenedetti, and I. G. Kevrekidis, Proc. Natl. Acad. Sci. U.S.A. 107, 13597 (2010). 10.1073/pnas.1003293107
- (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 13597
- Ferguson, A.L.¹ Panagiotopoulos, A.Z.² Debenedetti, P.G.³ Kevrekidis, I.G.⁴

20
- 49749151039
- 10.1063/1.2968610
- W. M. Brown, S. Martin, S. N. Pollock, E. A. Coutsias, and J.-P. Watson, J. Chem. Phys. 129, 064118 (2008). 10.1063/1.2968610
- (2008) J. Chem. Phys. , vol.129 , pp. 064118
- Brown, W.M.¹ Martin, S.² Pollock, S.N.³ Coutsias, E.A.⁴ Watson, J.-P.⁵

21
- 77953851412
- 10.1063/1.3445267
- S. Martin, A. Thompson, E. A. Coutsias, and J.-P. Watson, J. Chem. Phys. 132, 234115 (2010). 10.1063/1.3445267
- (2010) J. Chem. Phys. , vol.132 , pp. 234115
- Martin, S.¹ Thompson, A.² Coutsias, E.A.³ Watson, J.-P.⁴

22
- 1842692143
- 10.1021/ja00839a011
- D. Cremer and J. A. Pople, J. Am. Chem. Soc. 97, 1354 (1975). 10.1021/ja00839a011
- (1975) J. Am. Chem. Soc. , vol.97 , pp. 1354
- Cremer, D.¹ Pople, J.A.²

23
- 33846946504
- 10.1063/1.2432340
- D. Branduardi, F. L. Gervasio, and M. Parrinello, J. Chem. Phys. 126, 054103 (2007). 10.1063/1.2432340
- (2007) J. Chem. Phys. , vol.126 , pp. 054103
- Branduardi, D.¹ Gervasio, F.L.² Parrinello, M.³

24
- 62549151081
- 10.1021/ja806846q
- A. Berteotti, A. Cavalli, D. Branduardi, F. L. Gervasio, M. Recanatini, and M. Parrinello, J. Am. Chem. Soc. 131, 244 (2009). 10.1021/ja806846q
- (2009) J. Am. Chem. Soc. , vol.131 , pp. 244
- Berteotti, A.¹ Cavalli, A.² Branduardi, D.³ Gervasio, F.L.⁴ Recanatini, M.⁵ Parrinello, M.⁶

25
- 77952123773
- 10.1073/pnas.0911675107
- J. Pfaendtner, D. Branduardi, M. Parrinello, T. D. Pollard, and G. A. Voth, Proc. Natl. Acad. Sci. U.S.A. 97, 7299 (2010). 10.1073/pnas.0911675107
- (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 7299
- Pfaendtner, J.¹ Branduardi, D.² Parrinello, M.³ Pollard, T.D.⁴ Voth, G.A.⁵

26
- 27344454932
- GROMACS: Fast, flexible, and free
- DOI 10.1002/jcc.20291
- D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 26, 1701 (2005). 10.1002/jcc.20291 (Pubitemid 43076182)
- (2005) Journal of Computational Chemistry , vol.26 , Issue.16 , pp. 1701-1718
- Van Der Spoel, D.¹ Lindahl, E.² Hess, B.³ Groenhof, G.⁴ Mark, A.E.⁵ Berendsen, H.J.C.⁶

27
- 69349100797
- 10.1016/j.cpc.2009.05.011
- M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia, and M. Parrinello, Comput. Phys. Commun. 180, 1961 (2009). 10.1016/j.cpc.2009.05.011
- (2009) Comput. Phys. Commun. , vol.180 , pp. 1961
- Bonomi, M.¹ Branduardi, D.² Bussi, G.³ Camilloni, C.⁴ Provasi, D.⁵ Raiteri, P.⁶ Donadio, D.⁷ Marinelli, F.⁸ Pietrucci, F.⁹ Broglia, R.A.¹⁰ Parrinello, M.¹¹

28
- 7544226311
- PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
- DOI 10.1107/S0907444904011679
- A. W. Schuettelkopf and D. M. F. van Aalten, Acta Crystallogr. D 60, 1355 (2004). 10.1107/S0907444904011679 (Pubitemid 41079731)
- (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.8 , pp. 1355-1363
- Schuttelkopf, A.W.¹ Van Aalten, D.M.F.²

29
- 2942532422
- 10.1002/jcc.20035
- J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, J. Comput. Chem. 25, 1157 (2004). 10.1002/jcc.20035
- (2004) J. Comput. Chem. , vol.25 , pp. 1157
- Wang, J.¹ Wolf, R.M.² Caldwell, J.W.³ Kollman, P.A.⁴ Case, D.A.⁵

30
- 3042524904
- 10.1021/j100142a004
- C. I. Bayly, P. Cieplak, W. Cornell, and P. A. Kollman, J. Phys. Chem. 97, 10269 (1993). 10.1021/j100142a004
- (1993) J. Phys. Chem. , vol.97 , pp. 10269
- Bayly, C.I.¹ Cieplak, P.² Cornell, W.³ Kollman, P.A.⁴

31
- 70450206724
- Revision A.02, Gaussian Inc., Wallingford, CT
- M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 09, Revision A.02, Gaussian Inc., Wallingford, CT, 2004.
- (2004) GAUSSIAN 09
- Frisch, M.J.¹ Trucks, G.W.² Schlegel, H.B.³

32
- 17444412296
- Assessing the accuracy of metadynamics
- DOI 10.1021/jp045424k
- A. Laio, A. Rodriguez-Fortea, F. L. Gervasio, M. Ceccarelli, and M. Parrinello, J. Phys. Chem. B 109, 6714 (2005). 10.1021/jp045424k (Pubitemid 40538439)
- (2005) Journal of Physical Chemistry B , vol.109 , Issue.14 , pp. 6714-6721
- Laio, A.¹ Rodriguez-Fortea, A.² Gervasio, F.L.³ Ceccarelli, M.⁴ Parrinello, M.⁵

33
- 0002587756
- 10.1039/tf9383400041
- H. Eyring, Trans. Faraday Soc. 34, 41 (1938). 10.1039/tf9383400041
- (1938) Trans. Faraday Soc. , vol.34 , pp. 41
- Eyring, H.¹

34
- 84855304590
- See supplementary material at http://dx.doi.org/10.1063/1.3660208 E-JCPSA6-135-054142 for video sequences illustrating the progress of molecular dynamics and metadynamics.

35
- 67549127330
- 10.1063/1.3147642
- M. Sega, E. Autieri, and F. Pederiva, J. Chem. Phys. 130, 225102 (2009). 10.1063/1.3147642
- (2009) J. Chem. Phys. , vol.130 , pp. 225102
- Sega, M.¹ Autieri, E.² Pederiva, F.³

36
- 75149117767
- 10.1016/j.carres.2009.12.011
- V. Spiwok, B. Krlov, and I. Tvaroka, Carbohydr. Res. 345, 530 (2010). 10.1016/j.carres.2009.12.011
- (2010) Carbohydr. Res. , vol.345 , pp. 530
- Spiwok, V.¹ Krlov, B.² Tvaroka, I.³

37
- 79959951675
- 10.2174/157019311796197364
- M. M. Kuttel, Mini-Rev. Org. Chem. 8, 256 (2011). 10.2174/ 157019311796197364
- (2011) Mini-Rev. Org. Chem. , vol.8 , pp. 256
- Kuttel, M.M.¹

38
- 84899009769
- Global versus local methods in nonlinear dimensionality reduction
- edited by S. Backer, S. Thurn, and K. Obermayer (MIT Press, Cambridge, MA)
- V. de Silva and J. B. Tenenbaum, Global versus local methods in nonlinear dimensionality reduction, in Advances in Neural Information Processing Systems 15, edited by, S. Backer, S. Thurn, and, K. Obermayer, (MIT Press, Cambridge, MA, 2003), pp. 705-712.
- (2003) Advances in Neural Information Processing Systems 15 , pp. 705-712
- De Silva, V.¹ Tenenbaum, J.B.²

39
- 84862616884
- FastMap, MetricMap, and Landmark MDS are all Nyström Algorithms
- (The Society for Artificial Intelligence and Statistics, New Jersey)
- J. C. Platt, FastMap, MetricMap, and Landmark MDS are all Nyström Algorithms., in Proceedings of 10th International Workshop on Artificial Intelligence and Statistics, Barbados, 6-8 January 2005 (The Society for Artificial Intelligence and Statistics, New Jersey, 2005).
- (2005) Proceedings of 10th International Workshop on Artificial Intelligence and Statistics, Barbados, 6-8 January 2005
- Platt, J.C.¹

40
- 84855319827
- For more information about Pysomasee; Mayavi2, see http://code.enthought. com/projects/mayavi/; and PoVRay 3.6.1, see http://www.povray.org
- For more information about Pysomap see http://web.vscht.cz/spiwokv/ pysomap/; Mayavi2, see http://code.enthought.com/projects/mayavi/; and PoVRay 3.6.1, see http://www.povray.org.

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.