354
Views
62
CrossRef citations to date
0
Altmetric
Miscellany

The multiscale challenge for biomolecular systems: coarse-grained modeling

, &
Pages 211-218 | Received 01 Jan 2006, Accepted 01 Feb 2006, Published online: 31 Jan 2007

References

  • Goetz , R. and Lipowsky , R. 1998 . Computer simulations of bilayer membranes: self-assembly and interfacial tension . J. Chem. Phys. , 108 : 7397
  • Marrink , S.J. and Mark , A.E. 2003 . Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles . J. Am. Chem. Soc. , 125 : 15233
  • Shelley , J.C. and Shelley , M.Y. 2000 . Computer simulation of surfactant solutions . Curr. Opin. Colloid Interface Sci. , 5 : 101
  • Smit , B. , Esselink , K. , Hilbers , P.A. , van Os , N.M. , Rupert , L.A.M. and Szleifer , I. 1993 . Computer-simulations of surfactant self-assembly . Langmuir , 9 : 9
  • M.J. Stevens, J.H. Hoh, T.B. Woolf. Insights into the molecular mechanism of membrane fusion from simulation: evidence for the association of splayed tails. Phys. Rev. Lett., 91, 188102 (2003).
  • Shelley , J.C. , Shelley , M.Y. , Reeder , R.C. , Bandyopadhyay , S. and Klein , M.L. 2001 . Simulations of phospholipids using a coarse grain model . J. Phys. Chem. B , 105 : 4464
  • H. Meyer, O. Biermann, R. Faller, D. Reith, F. Muller-Plathe. Coarse graining of nonbonded inter-particle potentials using automatic simplex optimization to fit structural properties. J. Chem. Phys., 113, 6264 (2000).
  • Murtola , T. , Falck , E. , Patra , M. , Karttunen , M. and Vattulainena , I. 2004 . Coarse-grained model for phospholipid/cholesterol bilayer . J. Chem. Phys. , 121 : 9156
  • Izvekov , S. and Voth , G.A. 2005 . A multiscale coarse-graining method for biomolecular systems . J. Phys. Chem. B , 109 : 2469
  • Chu , J.-W. and Voth , G.A. 2006 . Coarse-grained modeling of the actin filament derived from atomistic-scale simulations . Biophys. J. , In press
  • Izvekov , S. , Parrinello , M. , Burnham , C.J. and Voth , G.A. 2004 . Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching . J. Chem. Phys. , 120 : 10896
  • Ayton , G.S. and Voth , G.A. 2002 . Bridging microscopic and mesoscopic simulations of lipid bilayers . Biophys. J. , 83 : 3357
  • Brooks , B.R. 1995 . Hatmonic analysis of large systems. I. Methodology . J. Comput. Chem. , 16 : 1522
  • Smondyrev , A.M. and Berkowitz , M.L. 1999 . United atom force field for phospholipid membranes: constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system . J. Comput. Chem. , 20 : 531
  • Jorgensen , W.L. , Chandrasekhar , J. , Madura , J.D. , Impey , R.W. and Klein , M.L. 1983 . Comparison of simple potential functions for simulating liquid water . J. Chem. Phys. , 79 : 926
  • Forester , T.R. and Smith , W. 1995 . “ DL_POLY user manual ” . In CCLRC , Warrington, UK : Daresbury Laboratory .
  • Howard , J. 2001 . Mechanics of Motor Proteins and the Cytoskeleton , Sunderland : Sinauer Associates, Inc. .
  • Korn , E.D. 1982 . Actin polymerization and its regulation by proteins from nonmuscle cells . Physiological Reviews , 62 : 672
  • Graceffa , P. and Dominguez , R. 2003 . Crystal structure of monomeric actin in the ATP state – structural basis of nucleotide-dependent actin dynamics . J. Biol. Chem. , 278 : 34172
  • Holmes , K.C. , Popp , D. , Gebhard , W. and Kabsch , W. 1990 . Atomic model of the actin filament . Nature , 347 : 44
  • Holmes , K.C. , Popp , D. , Gebhard , W. and Kabsch , W. 1990 . Atomic structure of the actin: DNase I complex . Nature , 347 : 37
  • Chu , J.W. and Voth , G.A. 2005 . Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis . Proc. Natl. Acad. Sci. USA. , 102 : 13111
  • Isambert , H. , Venier , P. , Maggs , A.C. , Fattoum , A. , Kassab , R. , Pantaloni , D. and Carliers , M.F. 1995 . Flexibility of actin filaments derived from thermal fluctuations . J. Biol. Chem. , 12 : 11437

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.