Full-text resources of PSJD and other databases are now available in the new Library of Science.
Visit https://bibliotekanauki.pl

PL EN


Preferences help
enabled [disable] Abstract
Number of results

Journal

2009 | 58 | 1-2 | 43-48

Article title

Symulacje dynamiki molekularnej biomolekuł na progu XXI wieku

Authors

Content

Title variants

EN
Molecular dynamics simulations of biomolecules at the beginning of the 21st century

Languages of publication

PL EN

Abstracts

EN
Computer simulations have become a mature and useful method in studies of molecules of life. As a part of structural bioinformatics carefully planned numerical experiments provide unique data on dynamics and properties of biomolecules. In this article a review of the state of art of molecular dynamics (MD) studies is presented. Current trends involving the steered MD, milestoning and coarse grained MD are described and some examples of MD applications in bio- and nano-technology are presented. The progress in hardware, such as parallel computing and purpose-built processors, is also addressed.

Keywords

Journal

Year

Volume

58

Issue

1-2

Pages

43-48

Physical description

Dates

published
2009

Contributors

  • Zespół Teoretycznej Biofizyki Molekularnej, Instytut Fizyki, Uniwersytet M. Kopernika w Toruniu, Grudziądzka 5/7, 87-100 Toruń, Polska

References

  • Adcock S. A., McCammon J. A., 2006. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106, 1589-1615.
  • Berendsen H. J. C. (ed.), 1976. Proceedings of the CECAM Workshop on models for protein dynamics. CECAM, Orsay, France,1-304.
  • Borell B., 2008. Chemistry: power play. Nature 451, 240-243.
  • Chu J. -w., Ayton G. S., Izvekov S., Voth G. A., 2007. Emerging methods for multiscale simulation of biomolecular systems. Mol. Phys. 105, 167-175.
  • Dal Peraro M., Ruggerone P., Raugei S., Gervasi F. L., Carloni P., 2007. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr. Opin. Struct. Biol. 17, 149-156.
  • Elber R., 2005. Long-timescale simulation methods. Curr. Opin. Struct. Biol. 15, 151-156.
  • Elcock A. H., Sept D., Mccammon J. A., 2001. computer simulation of protein−protein interactions. J. Phys. Chem. B 105, 1504-1518.
  • Freddolino P. L., Arkhipov A. S., Larson S. B., Mcpherson A., Schulten K., 2006. Molecular Dynamics simulations of the complete satellite Tobacco Mosaic Virus. Structure 14, 437-449.
  • Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C., 2006. Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins: Struct. Funct. Bioinform. 65, 712-725.
  • Jensen M. Ø., Dror R.o., Xu H., Borhani D. W., Arkin I. T., Eastwood M. P., Shaw D. E., 2008. Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens. Proc. Nat. Acad. Sci. USA 105, 14430-14435.
  • Klein M. L., Shinoda W., 2008. Large-scale molecular dynamics simulations of self-assembling systems. Science 321, 798-800.
  • Khurana E., Devane R. H., Kohlmeyer A., Klein M. L., 2008. Probing peptide nanotube self-assembly at a liquid−liquid interface with coarse-grained molecular dynamics. Nano Lett. 8, 3626-3630.
  • Kubiak K., Nowak W., 2008. Molecular dynamics simulations of the photoactive protein nitrile hydratase. Biophys. J. 94, 3824-3838.
  • Leach A., 2001. Molecular Modelling: Principles and Applications. (2nd Edition) Prentice Hall.
  • Liwo A., Czaplewski C., Ołdziej S., Scheraga H. A., 2008. Computational techniques for efficient conformational sampling of proteins. Curr. Opin. Struct. Biol. 18, 134-139.
  • Miller B. T., Singh R. P, Klauda J. B., Hodoscek M., Brooks B. R., Woodcock H. L., 2008. CHARMMing: A new, flexible web portal for CHARMM. J. Chem. Inf. Model. 48, 1920-1929.
  • Nowak W., Marszalek P., 2005. Molecular dynamics simulations of single molecule atomic force microscope experiments. [W:] Current Trends in Computational Chemistry. Leszczynski J. (red.). World Scientific, 47-83.
  • Orlowski S., Nowak W., 2008. Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin. Biosystems 94, 263-266.
  • >Orozco M., Noy A., Pérez A., 2008. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr. Opin. Struct. Biol. 18, 185-193.
  • Pepłowski Ł., Kubiak K., Nowak W., 2008. Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chem. Phys. Lett. 467, 144-149.
  • Petrov A. S., Harvey S. C., 2008. Packaging double-helical DNA into viral capsids: structures, forces, and energetics. Biophys. J. 95, 497-502.
  • Romanowska J., Setny P., Trylska J., 2008. Molecular dynamics study of the ribosomal A-site. J. Phys. Chem. B.112, 15227-15243.
  • Phillips, J. C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kalé L., Schulten K., 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802
  • Sen S., Andreatta D., Ponomarev S. Y., Beveridge D. L., Berg M. A., 2009. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J. Am. Chem. Soc. 131, 1724-1735.
  • Showalter S. A., Brüschweiler R., 2007. validation of molecular dynamics simulations of biomolecules using nmr spin relaxation as benchmarks: application to the AMBER99SB force field. J. Chem. Theory Comput. 3, 961-975.
  • Simms A. M., Toofanny R. D., Kehl C., Benson N. C., Daggett V., 2008. Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations. Protein Eng. Des. Sel. 21, 369-377.
  • Stone J. E., Phillips J. C., Freddolino P. L., Hardy D. J., Trabuco L. G., Schulten K., 2007. Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28, 2618-2640.
  • Van Der Kamp M. W., Shaw K. E., Woods Ch. J., Mulholland A. J., 2008. Biomolecular simulation and modelling: status, progress and prospects. J. R. Soc. Interface 5, 173-190.
  • Van Gunsteren W. F., Bakowies D., Baron R., Chandrasekhar I., Christem M., Daura X., Gee P., Geerke D. P., Alice Gättli A., Hünenberger P. H., Kastenholz M. A., Oostenbrink C., Schenk M., Trzesniak D., Van Der Vegt N. F. A., Yu H. B., 2006. Biomolecular modeling: goals, problems, perspectives. Angewandte Chemie Int. Ed. 45, 4064-4092.
  • Warshel A., 2003. Computer simulations of enzyme catalysis: methods, progress, and insights. Annu. Rev. Biophys. Biomol. Struct. 32, 425-443.
  • Warshel A., Kato M., Pisliakov A. V., 2007. Polarizable force fields: history, test cases, and prospects. J. Chem. Theory Comput. 3, 2034-2045.

Document Type

Publication order reference

Identifiers

YADDA identifier

bwmeta1.element.bwnjournal-article-ksv58p43kz
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.