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

Blau, C.; Grubmüller, H.

doi:10.1016/j.cpc.2013.07.018

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Journal Article

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

MPS-Authors

/persons/resource/persons14859

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

/persons/resource/persons15155

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

External Resource

http://www.sciencedirect.com/science/article/pii/S0010465513002464/pdfft?md5=1bce04b3367f39da924e273d9a2b779f&pid=1-s2.0-S0010465513002464-main.pdf
(Publisher version)

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

1900284.pdf
(Publisher version), 481KB

Supplementary Material (public)

There is no public supplementary material available

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: https://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.