g_contacts: Fast contact search in bio-molecular ensemble data
2013 | journal article
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Details
- Authors
- Blau, Christian ; Grubmüller, Helmut
- 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 run-time, in contrast to the complexity of a brute-force approach.
- Issue Date
- 2013
- Journal
- Computer Physics Communications
- ISSN
- 0010-4655
- Language
- English