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Том 6   Выпуск 1   Год 2011
Данилкович Алексей Викторович, Тихонов Дмитрий Анатольевич, Соболев Егор Васильевич, Шадрина Татьяна Евгеньевна, Удовиченко Игорь Петрович

К вопросу о выборе потенциальных полей для изучения молекулярной динамики ионных пептидов и их димеров

Математическая биология и биоинформатика. 2011;6(1):53-62.

doi: 10.17537/2011.6.53.

Список литературы

  1. Van Gunsteren WF, Dolenc J, Mark AE. Molecular simulation as an aid to experimentalists. Current Opinions in Structural Biology. 2008;18:149-153. doi: 10.1016/j.sbi.2007.12.007
  2. Mackerell AD. Empirical force fields for biological macromolecules: overview and issues. Journal of Computational Chemistry. 2004;25:1584-1604. doi: 10.1002/jcc.20082
  3. Jorgensen WL, Tirado-Rives J. Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proceedings of National Academy of Sciences of the USA. 2005;102:6665-6670. doi: 10.1073/pnas.0408037102
  4. Van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NF, Yu HB. Biomolecular modeling: goals, problems, perspectives. Angewandte Chemie International Edition. 2006;45(25):4064-4092. doi: 10.1002/anie.200502655
  5. Sorin EJ, Rhee YM, Shirts MR, Pande VS The solvation interface is a determining factor in peptide conformational preferences. Journal of Molecular Biology. 2006;356:248-256. doi: 10.1016/j.jmb.2005.11.058
  6. Hess B, van der Vegt NFA. Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models. Journal of Physical Chemistry B. 2006;110:17616-17626. doi: 10.1021/jp0641029
  7. Reif MM, Kräutler V, Kastenholz MA, Daura X, Hünenberger PH. Molecular dynamics simulations of a reversibly folding β-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions. Journal of Physical Chemistry B. 2009;113(10):3112-3128. doi: 10.1021/jp807421a
  8. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 2003;24(16):1999-2012. doi: 10.1002/jcc.10349
  9. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins. 2006;65(3):712-725. doi: 10.1002/prot.21123
  10. Feig M, MacKerell A, Brooks C. Force field influence on the observation of π-helical protein structures in molecular dynamics simulations. Journal of Computational Chemistry B. 2003;107:2831-2836.
  11. Oostenbrink C, Villa A, Mark AE, Gunsteren WFV. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry. 2004;25:1656-1676. doi: 10.1002/jcc.20090
  12. Kaminski G, Friesner R, Tirado-Rives J, Jorgensen W. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. Journal of Physical Chemistry B. 2001;105:6474-6487. doi: 10.1021/jp003919d
  13. Rueda M, Ferrer-Costa C, Meyer T, Pérez A, Camps J, Hospital A, Gelpí JL, Orozco M. A consensus view of protein dynamics. Proceedings of National Academy of Sciences of the USA. 2007;104(3):796-801. doi: 10.1073/pnas.0605534104
  14. Ferrara P, Apostolakis J, Caflisch A. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. Journal of Physical Chemistry B. 2000;104:5000-5010. doi: 10.1021/jp994157t
  15. Fersht AR, Daggett V. Protein folding and unfolding at atomic resolution. Cell. 2002;108:573-582. doi: 10.1016/S0092-8674(02)00620-7
  16. Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. Journal of American Chemical Society. 2002;124:11258-11259. doi: 10.1021/ja0273851
  17. Snow C.D., Nguyen H., Pande V.S., Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics molecular dynamics simulations. Nature. 2002;420:102-106. doi: 10.1038/nature01160
  18. Snow CD, Zagrovic B, Pande VS. The Trp cage folding kinetics and unfolded state topology via molecular dynamics simulations. Journal of American Chemical Society. 2002;124:14548-14549. doi: 10.1021/ja028604l
  19. Wu X, Brooks BR. β-hairpin folding mechanism of a nineresidue peptide revealed from molecular dynamics simulations in explicit water. Biophysical Journal. 2002;86:1946-1958.
  20. Gnanakaran S, Nymeyer H, Portman J, Sanbonmatsu KY, Garcı́a AE. Peptide folding simulations. Current Opinions in Structural Biology. 2003;13(2):168-174. doi: 10.1016/S0959-440X(03)00040-X
  21. Zhang S. Fabrication of novel biomaterials through molecular self-assembly. Nature Biotechnology. 2003;21:1171-1178. doi: 10.1038/nbt874
  22. Munoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nature Structural and Molecular Biology. 1994;1:399-409. doi: 10.1038/nsb0694-399
  23. Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Research. 2010;38:445-449. doi: 10.1093/nar/gkq311
  24. Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins. 2005;60(2):296-301. doi: 10.1002/prot.20573
  25. HyperChem® Computational Chemistry. Practical Guide – Theory and Method, HC 70-00-04-00. Gainesville: Hypercube Inc, 2002; 350 p.
  26. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 2005;26(16):1668-1688. doi: 10.1002/jcc.20290
  27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, and Klein ML. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983;79(2):926-935. doi: 10.1063/1.445869
  28. Kollman PA, Dixon R, Cornell W, Fox T, Chipot C, Pohorille A. The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: Computer Simulation of Biomolecular Systems. Van Gunsteren WF, Weiner PK, Wilkinson AJ, eds. Dordrecht: KLUWER/ESCOM, 1997;3:83-96.
  29. Lee MC, Duan Y. Distinguish protein decoys by using a scoring function based on a new Amber force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins. 2004;55:620-634. doi: 10.1002/prot.10470
  30. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;12:2577-2637.
  31. Onufriev A, Bashford D, Case DA. Modification of the Generalized Born Model Suitable for Macromolecules. Journal of Physical Chemistry B. 2000;104(15):3712-3720. doi: 10.1021/jp994072s
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2011;6(1):53-62
doi: 10.17537/2011.6.53
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы
Перевод на англ. яз.
Мат. биол. и биоинф.
2018;13(Suppl.):t29-t38
doi: 10.17537/2018.13.t29

Полный текст (англ., pdf)

 
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