Using sketch-map coordinates to analyze and bias molecular dynamics simulations

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 14, 2012, Pages 5196-5201

  Tribello, Gareth A ^a   Ceriotti, Michele ^b   Parrinello, Michele ^a  

^a UNIVERSITY OF LUGANO   (Switzerland)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CALCULATION; ENERGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROBABILITY; PROTEIN FOLDING; SIMULATION;

MOLECULAR DYNAMICS SIMULATION; PROBABILITY; PROTEIN FOLDING;

EID: 84859478167     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1201152109     Document Type: Article

References (45)

1. Garcia AE (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68:2696-2699.
2. Amadei A, Linssen ABM, Berendsen HJC (1993) Essential dynamics of proteins. Proteins Struct Funct Genet 17:412-425. (Pubitemid 23358549)
3. Piana S, Laio A (2008) Advillin folding takes place on a hypersurface of small dimensionality. Phys Rev Lett 101:208101.
4. Hegger R, Altis A, Nguyen PH, Stock G (2007) How complex is the dynamics of peptide folding? Phys Rev Lett 98:028102.
5. Wales DJ (2003) Energy Landscapes (Cambridge Univ Press, Cambridge, UK).
6. Shaw DE, et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341-346.
7. Frenkel D, Smit B (2002) Understanding Molecular Simulation (Academic, San Diego).
8. Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13:1011-1012.
9. Dickson BM, Lelièvre T, Stoltz G, Legoll F, Fleurat-Lessard P (2010) Free energy calculations: An efficient adaptive biasing potential method. J Phys Chem B 114:5823-5830.
10. Bonomi M, Barducci A, Parrinello M (2009) Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. J Comput Chem 30:1615-1621.
11. Dickson BM (2011) Approaching a parameter-free metadynamics. Phys Rev E 84:037701.
12. Laio A, Gervasio FL (2008) Metadynamics: A method to simulate rare events and reconstruct the free energy in biophysics, chemistry and materials sciences. Rep Prog Phys 71:126601.
13. Bonomi M, et al. (2009) Plumed: A portable plugin for free-energy calculations with molecular dynamics. Comput Phys Commun 180:1961-1972.
14. Barducci A, Bonomi M, Parrinello M (2011) Metadynamics. Wiley Interdiscip Rev: Comput Mol Sci 1:826-843.
15. Tribello GA, Ceriotti M, Parrinello M (2010) A self-learning algorithm for biased molecular dynamics. Proc Natl Acad Sci USA 107:17509-17514.
16. Ceriotti M, Tribello GA, Parrinello M (2011) Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci USA 108:13023-13029.
17. Geissler PL, Dellago C, Chandler D (1999) Kinetic pathways of ion pair dissociation in water. J Phys Chem B 103:3706-3710. (Pubitemid 129702423)
18. Cox TF, Cox MAA (1994) Multidimensional Scaling (Chapman & Hall, London).
19. Tenenbaum JB, de Silva V, Langford JC (2000) A global geometric framework for nonlinear dimensionality reduction. Science 290:2319-2323. (Pubitemid 32041577)
20. Das P, Moll M, Stamati H, Kavraki LE, Clementi C (2006) Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci USA 103:9885-9890. (Pubitemid 43993592)
21. Schölkopf B, Smola A, Müller KR (1998) Nonlinear component analysis as a kernel eigenvalue problem. Neural Comput 10:1299-1319.
22. Schölkopf B, Smola A, Muller KR (1999) Advances in Kernel Methods Support Vector Learning (MIT Press, Cambridge, MA), pp 327-352.
23. Coifman RR, et al. (2005) Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods. Proc Natl Acad Sci USA 102:7432-7437. (Pubitemid 40740989)
24. Coifman RR, Lafon S (2006) Diffusion maps. Applied and Computational Harmonic Analysis, Diffusion Maps 21:5-30.
25. Belkin M, Niyogi P (2003) Laplacian eigenmaps for dimensionality reduction and data representation. Neural Comput 15:1373-1396. (Pubitemid 37049796)
26. Ferguson AL, Panagiotopoulos AZ, Debenedetti PG, Kevrekidis IG (2010) Systematic determination of order parameters for chain dynamics using diffusion maps. Proc Natl Acad Sci USA 107:13597-13602.
27. Rohrdanz MA, Zheng W, Maggioni M, Clementi C (2011) Determination of reaction coordinates via locally scaled diffusion map. J Chem Phys 134:124116.
28. Donoho DL, Grimes C (2002) When does Isomap recover the natural parameterization of families of articulated images? (Department of Statistics, Stanford University), Technical Report No. 2002-27.
29. Donoho DL, Grimes C (2003) Hessian eigenmaps: Locally linear embedding techniques for high-dimensional data. Proc Natl Acad Sci USA 100:5591-5596. (Pubitemid 36576852)
30. Branduardi D, Gervasio FL, ParrinelloM(2007) From a to b in free energy space. J Chem Phys 126:054103.
31. Spiwok V, Kralova B (2011) Metadynamics in the conformational space nonlinearly dimensionally reduced by isomap. J Chem Phys 135:224504.
32. Laio A, Parrinello M (2002) Escaping free energy minima. Proc Natl Acad Sci USA 99:12562-12566.
33. Barducci A, Bussi G, Parrinello M (2008) Well tempered metadynamics: A smoothly converging and tunable free energy method. Phys Rev Lett 100:020603.
34. Mortenson PN, Evans DA, Wales DJ (2002) Energy landscapes of model polyalanines. J Chem Phys 117:1363-1376.
35. Dill KA, Ozkan SB, Shell MS, Weikl TR (2008) The protein folding problem. Annu Rev Biophys 37:289-316.
36. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics for protein folding. Chem Phys Lett 314:141-151. (Pubitemid 129556751)
37. Hansmann UE (1997) Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 281:140-150.
38. 2 hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc 128:13435-13441.
39. Krivov SV, KarplusM(2002) Free energy disconnectivity graphs: Application to peptide models. J Chem Phys 117:10894-10903.
40. Gfeller D, De Los Rios P, Caflisch A, Rao F (2007) Complex network analysis of freeenergy landscapes. Proc Natl Acad Sci 104:1817-1822. (Pubitemid 46239862)
41. Tribello GA, Cuny J, Eshet H, Parrinello M (2011) Exploring the free energy surfaces of clusters using reconnaissance metadynamics. J Chem Phys 135:114109.
42. Press WH, Teukolosky SA, VetterlingWT, Flannery BP (2007) Numerical Recipes: The Art of Scientific Computing (Cambridge Univ Press, Cambridge, UK).
43. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) Gromacs 4: Algorithms for highly efficient, load-balanced and scalable molecular simulation. J Chem Theory Comput 4:435-447.
44. Kollman PA (1996) Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Acc of Chem Res 29:461-469.
45. Ceriotti M, Bussi G, Parrinello M (2010) Colored-noise thermostats à la carte. J Chem Theory Comput 6:1170-1180.