Long-timescale simulation methods

Current Opinion in Structural Biology

Volumn 15, Issue 2, 2005, Pages 151-156

  Elber, Ron ^a  

^a Upson Hall 4130 ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN; LIGAND; PROTEIN;

CONFORMATIONAL TRANSITION; MACROMOLECULE; MATHEMATICAL COMPUTING; METHODOLOGY; MODEL; PRIORITY JOURNAL; REVIEW; SIMULATION;

EID: 17044425870     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.02.004     Document Type: Review

References (47)

1. Q. Ma, J.A. Izaguirre, and R.D. Skeel Verlet-I/r-RESPA/Impulse is limited by non-linear instabilities SIAM J Comput 24 2003 1951 1973 An interesting negative paper suggesting that we are at a 'theoretical limit' with regard to solving initial value problems.
2. M. Tuckerman, B.J. Berne, and G.J. Martyna Reversible multiple time scale molecular dynamics J Chem Phys 97 1992 1990 2001
3. D. Barash, L.J. Yang, X. Qian, and T. Schlick Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms J Comput Chem 24 2003 77 88
4. C. Xu, D. Tobi, and I. Bahar Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<->R2 transition J Mol Biol 333 2003 153 168 A new interesting direction for elastic networks. The authors attempt to interpolate between quadratic basins of elastic networks to estimate directions of transitional events. Although such interpolations were used in the past with harmonic analysis of atomic models, the extension and success of drastically simplified models is intriguing.
5. M.M. Tirion Large amplitude elastic motions in proteins from a single parameter atomic analysis Phys Rev Lett 77 1996 1905 1908
6. I. Bahar, B. Erman, T. Haliloglu, and R.L. Jernigan Efficient characterization of collective motions and interresidue correlations in proteins by low resolution simulations Biochemistry 36 1997 13512 13523
7. T.C. Flynn, and J.P. Ma Theoretical analysis of twist/bond ratio and mechanical moduli of bacterial flagellar and filament Biophys J 86 2004 3204 3210 An amusing application of a continuum/elastic description to a system that goes beyond typical molecular scales.
8. R. Elber, and M. Karplus Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin Science 235 1987 318 321
9. J. Pillardy, A. Liwo, M. Groth, and H.A. Scheraga An efficient deformation-based global optimization method for off-lattice polymer chains: self-consistent basin-to-deformed-basin mapping (SCBDBM). Application to united-residue polypeptide chains J Phys Chem B 103 1999 7353 7366
10. I. Andricioaei, and J.E. Straub Global optimization using bad derivatives: derivative-free method for molecular energy minimization J Comput Chem 19 1998 1445 1455
11. T.W. Whitfield, and J.E. Straub Gravitational smoothing as a global optimization strategy J Comput Chem 23 2002 1100 1103
12. B.W. Church, and D. Shalloway Top-down free-energy minimization on protein potential energy landscapes Proc Natl Acad Sci USA 98 2001 6098 6103
13. G.M. Torrie, and J.P. Valleau Non-physical sampling distributions in Monte-Carlo free energy estimation - umbrella sampling J Comput Phys 23 1977 187
14. Y. Peng, U.H. Hansmann, and N.A. Alves Solution effects and the order of the helix-coil transition in polyalanine J Chem Phys 118 2003 2374 2380
15. A. Mitsutake, Y. Sugita, and Y. Okamoto Replica-exhange multicanonical and multicanonical replica exchange Monte Carlo simulations of peptides. I. Formulation and benchmarks J Chem Phys 118 2003 6664 6675
16. Y. Okamoto Protein folding simulations by simulated annealing and generalized-ensemble algorithms Progress of Theoretical Physics Supplement 138 2000 301 310
17. E.M. Muller, A. de Meijere, and H. Grubmüller Predicting unimolecular chemical reactions: chemical flooding J Chem Phys 116 2002 897 905
18. A.F. Voter, F. Montalenti, and T.C. Germann Extending the time scale in atomistic simulation of materials Annu Rev Mater Res 32 2002 321 346
19. 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
20. H. Jonsson, G. Mills, and K.W. Jacobsen Nudge elastic band method for finding minimum energy paths of transitions B.J. Berne G. Ciccotti D.F. Coker Classical and Quantum Dynamics in Condensed Phase Simulations 1998 World Scientific 385
21. J.W. Chu, B.L. Trout, and B.R. Brooks A super-linear minimization scheme for the nudged elastic band method J Chem Phys 119 2003 12708 12717
22. E. Weinan, R. Weiqing, and E. Vanden Eijnden String method for the study of rare events Phys Rev B 66 2002 52301
23. L.R. Pratt A statistical-method for identifying transition-states in high dimensional problems J Chem Phys 85 1986 5045 5048
24. R. Elber, and M. Karplus A method for determining reaction paths in large molecules: application to myoglobin Chem Phys Lett 139 1987 375 380
25. A. Ulitsky, and R. Elber A new technique to calculate steepest descent paths in flexible polyatomic systems J Chem Phys 92 1990 1510 1511
26. R. Czerminski, and R. Elber Self-avoiding walk between 2 fixed-points as a tool to calculate reaction paths in large molecular-systems Int J Quantum Chem 24 1990 167 186
27. R. Olender, and R. Elber Yet another look at the steepest descent path J Mol Struct THEOCHEM 398 1997 63 71
28. E. Weinan, and E. Vanden Eijnden Metastability, conformational dynamics, and transition pathways in complex systems S. Attinger P. Koumoutsakos Multiscale Modelling and Simulation vol 39 2004 Springer 35 68 [Series: Lecture Notes in Computational Science and Engineering]
29. M. Berkowitz, J.D. Morgan, J.A. McCammon, and J.H. Northrup Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate J Chem Phys 79 1983 5563 5565
30. R. Elber, and D. Shalloway Temperature dependent reaction coordinates J Chem Phys 128 2000 118 127
31. S.H. Huo, and J.E. Straub The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature J Chem Phys 107 1997 5000 5006
32. R. Olender, and R. Elber Calculation of classical trajectories with a very large time step: formalism and numerical examples J Chem Phys 105 1996 9299 9315
33. R. Elber, A. Ghosh, A. Cardenas, and H. Stern Bridging the gap between reaction pathways, long time dynamics and calculation of rates Adv Chem Phys 126 2003 93 129
34. D. Passerone, M. Ceccarelli, and M. Parrinello A concerted variational strategy for investigating rare events J Chem Phys 118 2003 2025 2032
35. A.E. Cardenas, and R. Elber Kinetics of cytochrome c folding: atomically detailed simulations Proteins 51 2003 245 257 This study presents approximate atomically detailed molecular dynamics trajectories for a highly complex folding process, with significant success in reproducing the order of events in protein folding.
36. A. Cardenas, and R. Elber Atomically detailed simulations of helix formation with the stochastic difference equation Biophys J 85 2003 2919 2939
37. P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler Transition path sampling: throwing ropes over rough mountain passes, in the dark Annu Rev Phys Chem 53 2002 291 318
38. C. Dellago, P.G. Bolhuis, F.S. Csajka, and D. Chandler Transition path sampling and the calculation of rate constants J Chem Phys 108 1998 1964 1977
39. P.G. Bolhuis Transition-path sampling of beta-hairpin folding Proc Natl Acad Sci USA 100 2003 12129 12134 A most impressive application of the transition path sampling approach to the folding of a model peptide (β hairpin).
40. R. Radhakrishnan, and T. Schlick Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing Proc Natl Acad Sci USA 101 2004 5970 5975
41. •].
42. • ] suggest a novel and interesting way to deal with corrugated surfaces with many, but relatively small, barriers that lead to long-timescale diffusion processes. An example of a study appropriate to this approach is the first step in protein folding, which includes chain collapse to the molten globule state.
43. V.S. Pande Simulations of the role of water in the protein folding mechanism Proc Natl Acad Sci USA 101 2004 6456 6461 An impressive and computationally expensive study of the role of waters in protein folding, using tens of thousands of independent trajectories on the author's unique computational resource.
44. V.S. Pande Meeting halfway on the bridge between protein folding theory and experiment Proc Natl Acad Sci USA 100 2003 3555 3556
45. V.S. Pande, I. Baker, J. Chapman, S.P. Elmer, S. Khaliq, S.M. Larson, Y.M. Rhee, M.R. Shirts, C.D. Snow, and E.J. Sorin Atomistic protein folding simulations on the sub millisecond time scale using worldwide distributed computing Biopolymers 68 2003 91 109
46. M.R. Shirts, J.W. Pitera, W.C. Swope, and V.S. Pande Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force field for proteins J Chem Phys 119 2003 5740 5761
47. S.M. Larson, J.L. England, J.R. Desjarlais, and V.S. Pande Thoroughly sampling sequence space: large-scale protein design of structural ensembles Protein Sci 11 2002 2804 2813