A molecular simulation protocol to avoid sampling redundancy and discover new states

Biochimica et Biophysica Acta - General Subjects

Volumn 1850, Issue 5, 2015, Pages 889-902

  Bacci, Marco ^a   Vitalis, Andreas ^a   Caflisch, Amedeo ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Biomolecules; Enhanced sampling; Molecular dynamics; Scalable algorithm; Simulation convergence; Transition path

Indexed keywords

ACCURACY; ALPHA HELIX; ARTICLE; COMPUTER PROGRAM; CONFORMATION; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PHASE TRANSITION; PRIORITY JOURNAL; SAMPLING; SIMULATION; ALGORITHM; CHEMISTRY; KINETICS; METABOLISM; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; REPRODUCIBILITY; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

PROTEIN;

ALGORITHMS; KINETICS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 84923174409     PISSN: 03044165     EISSN: 18728006     Source Type: Journal    
DOI: 10.1016/j.bbagen.2014.08.013     Document Type: Article

References (71)

1. W.F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D.P. Geerke, A. Glättli, P.H. Hünenberger, M.A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N.F.A. Van Der Vegt, and H.B. Yu Biomolecular modeling: goals, problems, perspectives Angew. Chem. Int. Ed. Engl. 45 2006 4064 4092
2. T. Schlick, R. Collepardo-Guevara, L.R. Halvorsen, S. Jung, and X. Xiao Biomolecular modeling and simulation: a field coming of age Q. Rev. Biophys. 44 2011 191 228
3. K. Lindorff-Larsen, S. Piana, R.O. Dror, and D.E. Shaw How fast-folding proteins fold Science 334 2011 517 520
4. M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652
5. S.D. Bond, and B.J. Leimkuhler Molecular dynamics and the accuracy of numerically computed averages Acta Num. 16 2007 1 65
6. R. Elber Long-timescale simulation methods Curr. Opin. Struct. Biol. 15 2005 151 156
7. H. Lei, and Y. Duan Improved sampling methods for molecular simulation Curr. Opin. Struct. Biol. 17 2007 187 191
8. D.M. Zuckerman Equilibrium sampling in biomolecular simulations Annu. Rev. Biophys. 40 2011 41 62
9. K. Klenin, B. Strodel, D.J. Wales, and W. Wenzel Modelling proteins: conformational sampling and reconstruction of folding kinetics Biochim. Biophys. Acta 1814 2011 977 1000
10. T. Schlick, E. Barth, and M. Mandziuk Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation Annu. Rev. Biophys. Biomol. Struct. 26 1999 181 222
11. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
12. A. Jain, N. Vaidehi, and G. Rodriguez A fast recursive algorithm for molecular dynamics simulation J. Comput. Phys. 106 1993 258 268
13. M.E. Tuckerman, G.J. Martyna, and B.J. Berne Molecular dynamics algorithm for condensed systems with multiple time scales J. Chem. Phys. 93 1990 1287 1291
14. R. Pomès, and J.A. McCammon Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation Chem. Phys. Lett. 166 1990 425 428
15. R. Das, and D. Baker Macromolecular modeling with Rosetta Annu. Rev. Biochem. 77 2008 363 382
16. E. Brini, E.A. Algaer, P. Ganguly, C. Li, F. Rodriguez-Ropero, and N.F.A. van der Vegt Systematic coarse-graining methods for soft matter simulations - a review Soft Matter 9 2013 2108 2119
17. M.G. Saunders, and G.A. Voth Coarse-graining methods for computational biology Annu. Rev. Biophys. 42 2013 73 93
18. H. Li, G. Li, B.A. Berg, and W. Yang Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces J. Chem. Phys. 125 2006 144902
19. E. Lyman, F.M. Ytreberg, and D.M. Zuckerman Resolution exchange simulation Phys. Rev. Lett. 96 2006 028105
20. G.M. Torrie, and J.P. Valleau Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling J. Comput. Phys. 23 1977 187 199
21. A. Laio, and M. Parrinello Escaping free-energy minima Proc. Natl. Acad. Sci. U. S. A. 99 2002 12562 12566
22. S. Singh, M. Chopra, and J.J. de Pablo Density of states-based molecular simulations Annu. Rev. Chem. Biomol. Eng. 3 2012 369 394
23. S. Park, and K. Schulten Calculating potentials of mean force from steered molecular dynamics simulations J. Chem. Phys. 120 2004 5946 5961
24. B. Roux The calculation of the potential of mean force using computer simulations Comp. Physiol. Commut. 91 1995 275 282
25. C. Neale, T. Rodinger, and R. Pomès Equilibrium exchange enhances the convergence rate of umbrella sampling Chem. Phys. Lett. 460 2008 375 381
26. W. Sinko, Y. Miao, C.A.F. de Oliveira, and J.A. McCammon Population based reweighting of scaled molecular dynamics J. Phys. Chem. B 117 2013 12759 12768
27. D. Hamelberg, J. Mongan, and J.A. McCammon Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J. Chem. Phys. 120 2004 11919 11929
28. R.H. Swendsen, and J.S. Wang Replica Monte Carlo simulation of spin glasses Phys. Rev. Lett. 57 1986 2607 2609
29. Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 314 1999 141 151
30. H. Nymeyer How efficient is replica exchange molecular dynamics? An analytic approach J. Chem. Theory Comput. 4 2008 626 636
31. K. Ostermeir, and M. Zacharias Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins Biochim. Biophys. Acta 1834 2013 847 853
32. D.M. Zuckerman, and E. Lyman A second look at canonical sampling of biomolecules using replica exchange simulation J. Chem. Theory Comput. 2 2006 1200 1202
33. E. Rosta, and G. Hummer Error and efficiency of replica exchange molecular dynamics simulations J. Chem. Phys. 131 2009 165102
34. W. Zhang, and J. Chen Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions J. Chem. Theory Comput. 9 2013 2849 2856
35. W. Zheng, M. Andrec, E. Gallicchio, and R.M. Levy Simulating replica exchange simulations of protein folding with a kinetic network model Proc. Natl. Acad. Sci. U. S. A. 104 2007 15340 15345
36. S. Muff, and A. Caflisch ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations J. Phys. Chem. B 113 2009 3218 3226
37. D.A. Beck, G.W. White, and V. Daggett Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations J. Struct. Biol. 157 2007 514 523
38. P.G. Bolhuis, C. Dellago, D. Chandler, and P.L. Geissler Transition path sampling: throwing ropes over rough mountain passes, in the dark Annu. Rev. Phys. Chem. 53 2002 291 318
39. G. Henkelman, B.P. Uberuaga, and H. Jónsson A climbing image nudged elastic band method for finding saddle points and minimum energy paths J. Chem. Phys. 113 2000 9901 9904
40. W. E., W. Ren, and E. Vanden-Eijnden Finite temperature string method for the study of rare events J. Phys. Chem. B 2005 6688 6693
41. A.K. Faradjian, and R. Elber Computing time scales from reaction coordinates by milestoning J. Chem. Phys. 120 2004 10880 10889
42. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti String method in collective variables: minimum free energy paths and isocommittor surfaces J. Chem. Phys. 125 2006 024106
43. G.R. Bowman, K.A. Beauchamp, G. Boxer, and V.S. Pande Progress and challenges in the automated construction of Markov state models for full protein systems J. Chem. Phys. 131 2009 124101
44. J.D. Chodera, and F. Noé Markov state models of biomolecular conformational dynamics Curr. Opin. Struct. Biol. 25 2014 135 144
45. X. Huang, G.R. Bowman, S. Bacallado, and V.S. Pande Rapid equilibrium sampling initiated from nonequilibrium data Proc. Natl. Acad. Sci. U. S. A. 106 2009 19765 19769
46. N. Singhal, C.D. Snow, and V.S. Pande Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin J. Chem. Phys. 121 2004 415 425
47. V.S. Pande, I. Baker, J. Chapman, S.P. Elmer, S. Khaliq, S.M. Larson, Y.M. Rhee, M.R. Shirts, C.D. Snow, E.J. Sorin, and B. Zagrovic Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing Biopolymers 68 2002 91 109
48. T. Zhou, and A. Caflisch Free energy guided sampling J. Chem. Theory Comput. 8 2012 2134 2140
49. W. Zheng, M.A. Rohrdanz, and C. Clementi Rapid exploration of configuration space with diffusion-map-directed molecular dynamics J. Phys. Chem. B 117 2013 12769 12776
50. A. Dickson, and C.L. Brooks III WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm J. Phys. Chem. B 118 2014 3532 3542
51. C. Schütte, A. Fischer, W. Huisinga, and P. Deuflhard A direct approach to conformational dynamics based on hybrid Monte Carlo J. Comput. Phys. 151 1999 146 168
52. E. Vanden-Eijnden, and M. Venturoli Markovian milestoning with Voronoi tesselations J. Chem. Phys. 130 2009 194101
53. N. Blöchliger, A. Vitalis, and A. Caflisch A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems Comp. Physiol. Commut. 184 2013 2446 2453
54. D.J. Lockhart, and P.S. Kim Internal Stark effect measurement of the electric field at the amino terminus of an α helix Science 257 1992 947 951
55. S.D. Bond, B.B. Laird, and B.J. Leimkuhler The Nosé-Poincaré method for constant temperature molecular dynamics J. Comput. Phys. 151 1999 114 134
56. A. Vitalis, and A. Caflisch Efficient construction of mesostate networks from molecular dynamics trajectories J. Chem. Theory Comput. 8 2012 1108 1120
57. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38
58. A. Vitalis, and R.V. Pappu ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions J. Comput. Chem. 30 2009 673 699
59. A. Vitalis, and A. Caflisch 50 Years of Lifson-Roig models: application to molecular simulation data J. Chem. Theory Comput. 8 2012 363 373
60. G.A. Kaminski, R.A. Friesner, J. Tirado-Rives, and W.L. Jorgensen Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 105 2001 6474 6487
61. R.D. Skeel, and J.A. Izaguirre An impulse integrator for Langevin dynamics Mol. Phys. 100 2002 3885 3891
62. T. Kamada, and S. Kawai An algorithm for drawing general undirected graphs Inf. Process. Lett. 31 1989 7 15
63. T. Ichiye, and M. Karplus Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations Proteins Struct. Funct. Bioinforma. 11 1991 205 217
64. Y. Sugita, A. Kitao, and Y. Okamoto Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 113 2000 6042 6051
65. A. Vitalis, and R.V. Pappu Methods for Monte Carlo simulations of biomacromolecules Annu. Rep. Comput. Chem. 5 2009 49 76
66. S. Asmussen, P.W. Glynn, and H. Thorisson Stationarity detection in the initial transient problem ACM Trans. Model. Comput. Simul. 2 1992 130 157
67. A. Grossfield, and D.M. Zuckerman Quantifying uncertainty and sampling quality in biomolecular simulations Annu. Rep. Comput. Chem. 5 2009 23 48
68. C. Komalapriya, M. Thiel, M.C. Romano, N. Marwan, U. Schwarz, and J. Kurths Reconstruction of a system's dynamics from short trajectories Phys. Rev. E. 78 2008 066217
69. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T.R. Weikl Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations Proc. Natl. Acad. Sci. U. S. A. 106 2009 19011 19016
70. A. Grossfield, S.E. Feller, and M.C. Pitman Convergence of molecular dynamics simulations of membrane proteins Proteins Struct. Funct. Bioinforma. 67 2007 31 40
71. W.F. van Gunsteren, and A.E. Mark Validation of molecular dynamics simulation J. Chem. Phys. 108 1998 6109 6116