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Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations

Journal Article


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Abstract


  • Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.

Publication Date


  • 2007

Citation


  • Burden, C. J. & Oakley, A. J. (2007). Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations. Physical Biology, 4 (2), 79-90.

Scopus Eid


  • 2-s2.0-34447259836

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1936&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/897

Number Of Pages


  • 11

Start Page


  • 79

End Page


  • 90

Volume


  • 4

Issue


  • 2

Abstract


  • Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.

Publication Date


  • 2007

Citation


  • Burden, C. J. & Oakley, A. J. (2007). Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations. Physical Biology, 4 (2), 79-90.

Scopus Eid


  • 2-s2.0-34447259836

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1936&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/897

Number Of Pages


  • 11

Start Page


  • 79

End Page


  • 90

Volume


  • 4

Issue


  • 2