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Journal Article

g_contacts: Fast contact search in bio-molecular ensemble data.

MPS-Authors
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Blau,  C.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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Grubmüller,  H.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

Fulltext (public)

1900284.pdf
(Publisher version), 481KB

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Citation

Blau, C., & Grubmüller, H. (2013). g_contacts: Fast contact search in bio-molecular ensemble data. Computer Physics Communications, 184(12), 2856-2859. doi:10.1016/j.cpc.2013.07.018.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0015-0E81-8
Abstract
Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach.