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

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.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0015-0E81-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CB5E-D
Genre: Journal Article

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1900284.pdf (Publisher version), 481KB
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 Creators:
Blau, C.1, Author              
Grubmüller, H.1, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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Free keywords: Range search; Molecular dynamics; Decomposition scheme; Gromacs
 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.

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Language(s): eng - English
 Dates: 2013-07-292013-12
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.cpc.2013.07.018
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Title: Computer Physics Communications
Source Genre: Journal
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Pages: - Volume / Issue: 184 (12) Sequence Number: - Start / End Page: 2856 - 2859 Identifier: -