Adaptive spectral clustering for conformation analysis

AIP Conference Proceedings

Volumn 1281, Issue , 2010, Pages 1585-1588

  Haack, Fiete ^a   Röblitz, Susanna ^b   Scharkoi, Olga ^b   Schmidt, Burkhard ^c   Weber, Marcus ^b  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b ZUSE INSTITUTE BERLIN   (Germany)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

metastable conformation; molecular dynamics simulations; peptides; spectral clustering

Indexed keywords

EID: 79954481928     PISSN: 0094243X     EISSN: 15517616     Source Type: Conference Proceeding    
DOI: 10.1063/1.3498116     Document Type: Conference Paper

References (14)

1. M. Dellnitz, and O. Junge, SIAM J. Numer. Anal. 36, 491-515 (1999), URL http://www.jstor.org/stable/2587207.
2. C. Schütte, Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules, Habilitation thesis, Department of Mathematics and Computer Science, Freie Universität Berlin (1999), URL http://opus.kobv.de/zib/volltexte/1999/407/.
3. P. Deuflhard, W. Huisinga, A. Fischer, and C. Schütte, Lin. Alg. Appl. 315, 39-59 (2000), URL http://dx.doi.org/10.1016/S0024-3795(00)00095-1.
4. P. Deuflhard, "From Molecular Dynamics to Conformational Dynamics in Drug Design," in Trends in Nonlinear Analysis, edited by M. Kirkilionis, S. Krömker, R. Rannacher, and F. Tomi, Springer, 2003, pp. 269-287.
5. F. Haack, Representative Spectral Clustering for Large Data Sets applied to Gene Expression Data, Master's thesis, Freie Universität Berlin (2009), available from fiete.haack@uni-rostock.de.
6. M.Weber, and T. Galliat, Characterization of transition states in conformational dynamics using fuzzy sets, ZIB-Report 02-12, Zuse Institute Berlin (2002), URL http://opus.kobv.de/zib/volltexte/2002/680/.
7. S. Kube, and M. Weber, J. Chem. Phys. 126 (2007), URL http://dx.doi.org/10.1063/1.2404953.
8. D. Shepard, "A two-dimensional interpolation for irregularly spaced data," in Proc. 23rd ACM Nat. Conf., 1968, pp. 517-524.
9. J. Hartigan, and M. Wong, J. Royal Stat. Soc. 28, 100-108 (1979), URL http://www.jstor.org/stable/2346830.
10. H. Zhu, M. Blom, I. Compagnon, A. M. Rijs, S. Roy, and G. von Helden, Phys. Chem. Chem. Phys. 12, 3415-3425 (2010), URL http://dx.doi.org/10.1039/ b926413b.
11. A. Aubry, D. Bayeul, H. Brückner, N. Schiemann, and E. Benedetti, J. Pept. Sci. 4, 502 (1998), URL http://dx.doi.org/10.1002/(SICI)1099-1387(199812) 4:8〈502::AID-PSC171〉3.0.CO;2-N.
12. B. Di Blasio, V. Pavone, M. Saviano, A. Lombardi, F. Nastri, C. Pedone, E. Benedetti, M. Crisma, M. Anzolin, and C. Toniolo, J. Am. Chem. Soc. 114, 6273 (1992), URL http://dx.doi.org/10.1021/ja00042a001.
13. T. A. Halgren, J. Comput. Chem. 20, 730-748 (1999), URL http://dx.doi.org/10.1002/(SICI)1096-987X(199905)20:7〈730::AID-JCC8〉3. 0.CO;2-T.
14. S. Nosé, J. Chem. Phys. 81, 511-519 (1984), URL http://dx.doi.org/10.1063/1.447334.