g_contacts: Fast contact search in bio-molecular ensemble data

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• 作者：Christian Blau ; Helmut Grubmuller
• 关键词：Range search ; Molecular dynamics ; Decomposition scheme ; Gromacs
• 刊名：Computer Physics Communications
• 出版年：December, 2013
• 年：2013
• 卷：184
• 期：12
• 页码：2856-2859
• 全文大小：480 K

文摘

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.

Program summary

Program title: g_contacts

Catalogue identifier: AEQA_v1_0

Program summary URL:

Program obtainable from: CPC Program Library, Queen鈥檚 University, Belfast, N. Ireland

Licensing provisions: Standard CPC licence,

No. of lines in distributed program, including test data, etc.: 8945

No. of bytes in distributed program, including test data, etc.: 981604

Distribution format: tar.gz

Programming language: C99.

Computer: PC.

Operating system: Linux.

RAM: 鈮圫ize of input frame

Classification: 3, 4.14.

External routines: Gromacs 4.6[1]

Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off.

Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets.

Running time:

References:

[1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).