Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Olson, Mark A ^a,b   Lee, Michael S ^c  

^a UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c U S ARMY RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; INTERMETHOD COMPARISON; PROTEIN CONFORMATION; PROTEIN STRUCTURE; REPLICA EXCHANGE SIMULATION; SAMPLING; SIMULATION; TEMPERATURE; BIOLOGY; CHEMISTRY; MOLECULAR DYNAMICS; PROCEDURES; PROTEIN FOLDING; THERMODYNAMICS;

PROTEIN;

COMPUTATIONAL BIOLOGY; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; TEMPERATURE; THERMODYNAMICS;

EID: 84901297475     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096638     Document Type: Article

References (39)

1. Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols 5: 725-38.
2. Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, et al. (2009) Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 77 Suppl 9: 89-99.
3. MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, et al. (2011) Assessment of protein structure refinement in CASP. Proteins 79 Suppl 10: 74-90.
4. Nugent T, Cozzetto D, Jones DT (2013) Evaluation of predictions in the CASP10 model refinement category. Proteins. [Epub ahead of print].
5. Mirjalili V, Feig M (2013) Protein structure refinement through structure selection and averaging from molecular dynamics ensembles. J Chem Theory Comput 9: 1294-1303.
6. Mirjalili V, Noyes K, Feig M (2014) Physics based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins 82 Suppl 2: 196-207.
7. Olson MA, Lee MS (2013) Structure refinement of protein model decoys requires accurate side-chain placement. Proteins 81: 469-78.
8. Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE (2012) Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins 80: 2071-79.
9. Olson MA, Chaudhury S, Lee MS (2011) Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations. J Comput Chem 32: 3014-22.
10. Bhattacharya D, Cheng J (2013) 3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization. Proteins 81: 119-31.
11. Zhang J, Liang Y, Zhang Y (2011) Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure 19: 1784-95.
12. Xu D, Zhang J, Roy A, Zhang Y (2011) Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins 79 (Suppl. 10), 147-60.
13. Chen J, Brooks CL 3rd. (2007) Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 67: 922-30. (Pubitemid 46753939)
14. Larsen AB, Wagner JR, Jain A, Vaidehi N (2013) Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method. J Chem Inf Model. [Epub ahead of print].
15. Ishikawa Y, Sugita Y, Nishikawa T, Okamoto Y (2001) Ab initio replicaexchange Monte Carlo method for cluster studies. Chem Phys Lett 33: 199-206. (Pubitemid 33627956)
16. Predescu C, Predescu M, Ciobanu CV (2004) The incomplete beta function law for parallel tempering sampling of classical canonical systems. J Chem Phys 120: 4119-28.
17. Yeh IC, Lee MS, Olson MA (2008) Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models. J Phys Chem B 112: 15064-73.
18. Lee MS, Olson MA (2011) Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding. J Chem Phys 134: 244111-17.
19. Trebst S, Troyer M, Hansmann UH (2006) Optimized parallel tempering simulations of proteins. J Chem Phys 124: 174903-09.
20. Katzgraber G, Trebst S, Huse DA, Troyer M (2006) Feedback-optimized parallel tempering Monte Carlo. J Stat Mech Theory Exp P03018.
21. Spill YG, Bouvier G, Nilges M (2013) A convective replica-exchange method for sampling new energy basins. J Comput Chem 34: 132-40.
22. Olson MA, Lee MS (2013) Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models. J Comput Chem 34: 1785-93.
23. Wu X, Brook BR (2003) Self-guided Langevin dynamics simulation method. Chem Phys Letters 381: 512-518.
24. Lee MS, Olson MA (2010) Protein folding simulations combining self-guided Langevin dynamics and temperature-based replica exchange. J Chem Theory Comput 6: 2477-87.
25. Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21: 1087-1092.
26. I-TASSER Decoy Set-II website. Available: http://zhanglab.ccmb.med.umich. edu/decoys/decoy2.html. Accessed 2014 April 30.
27. Zhang J, Zhang Y (2010) A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One 5 e15386.
28. Krivov GG, Shapovalov MV, Dunbrack RL Jr (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77: 778-95.
29. Mackerell AD Jr, Feig M, Brooks CL 3rd (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-15.
30. Lee MS, Feig M, Salsbury FR Jr, Brooks CL 3rd (2003) New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem 24: 1348-56.
31. Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phy 23: 327-41.
32. Feig M, Karanicolas J, Brooks CL 3rd (2004) MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 22: 377-95. (Pubitemid 38510304)
33. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, et al. (2009) CHARMM: The biomolecular simulation program. J Comput Chem 30: 1545-1614.
34. Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Proteins Sci 11: 2714-26. (Pubitemid 35191145)
35. Zhou H, Skolnick J (2011) GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J 101: 2043-52.
36. Zhou R, Berne BJ (2002) Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water? Proc Natl Acad Sci USA 99: 12777-82.
37. Yeh I-C, Lee MS, Olson MA (2008) Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models. J Phys Chem B 112: 15064-15073.
38. Chaudhury S, Olson MA, Tawa G, Wallqvist A, Lee MS (2012) Efficient conformational sampling in explicit solvent using a hybrid replica exchange molecular dynamics method. J Chem Theory Comput 8: 677-687.
39. Zhang W, Chen J (2013) Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions. J Chem Theory Comput 9: 2849-56.