g_contacts: Fast contact search in bio-molecular ensemble data
g_contacts: Fast contact search in bio-molecular ensemble data
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DOI：
10.1016/j.cpc.2013.07.018
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发表时间：
2013-12-01
影响因子：
6.3
通讯作者：
Grubmuller, Helmut
中科院分区：
文献类型：
--
作者：
Blau, Christian;Grubmuller, Helmut
原子间的短程相互作用支配着许多生物分子过程。因此，在集成数据中识别密切的相互作用伙伴是结构生物学和计算生物物理学中的一项基本任务。联系人搜索可以被归结为一个典型的范围搜索问题，对于该问题已经开发了有效的算法。然而，这些都还没有适应大分子系综的背景，特别是在分子动力学(MD)框架下。这里实现了一个集合分解算法，它在最大O(N log(N))运行时检测所有接触的原子或残基，而不是暴力方法的O(N-2)复杂性。程序摘要程序标题：G_Contact目录标识符：AEQA_v1_0程序摘要URL：http://cpc.cs.qub.ac.uk/summaries/AEQA_v1_0.htmlProgram可从：CPC程序库，女王大学，贝尔法斯特，N爱尔兰获得。许可条款：标准CPC许可证，http://cpc.cs.qub.ac.uk/licence/licence.htmlNo.分布式程序中的行数，包括测试数据等：8945第分布式程序中的字节数，包括测试数据等：981604分布格式：tar.gz编程语言：C99计算机：PC操作系统：Linux.RAM：近似于输入帧的大小分类：3，4.14外部例程：Gromacs 4.6[1]问题的性质：找到比给定截止点更近的原子或残基。解决方法：通过将给定的原子集分解为不相交的子集，将距离计算中的距离排除在外。运行时间：
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(N log(N)) run-time, in contrast to the O(N-2) complexity of a brute-force approach.Program summaryProgram title: g_contactsCatalogue identifier: AEQA_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEQA_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 8945No. of bytes in distributed program, including test data, etc.: 981604Distribution format: tar.gzProgramming language: C99.Computer: PC.Operating system: Linux.RAM: approximate to Size of input frameClassification: 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: