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首页> 外文期刊>Multiscale modeling & simulation >Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity
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Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity

机译：缺乏整体结构相似性的新型多分辨方法在生物分子静电性质比较中的应用

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摘要

In this paper we present a method for the multiresolution comparison of biomolecular electrostatic potentials without the need for global structural alignment of the biomolecules. The underlying computational geometry algorithm uses multiresolution attributed contour trees (MACTs) to compare the topological features of volumetric scalar fields. We apply the MACTs to compute electrostatic similarity metrics for a large set of protein chains with varying degrees of sequence, structure, and function similarity. For calibration, we also compute similarity metrics for these chains by a more traditional approach based upon 3D structural alignment and analysis of Carbo similarity indices. Moreover, because the MACT approach does not rely upon pairwise structural alignment, its accuracy and efficiency promise to perform well on future large-scale classification efforts across groups of structurally diverse proteins. The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method; i.e., it is able to accurately cluster proteins into functionally relevant groups which demonstrate strong dependence on ligand binding sites. The results of the analyses are available from the linked web databases http://ccvweb.cres.utexas.edu/MolSignature/ and http://agave.wustl.edu/similarity/. The MACT analysis tools are available as part of the public domain library of the Topological Analysis and Quantitative Tools (TAQT) from the Center of Computational Visualization at the University of Texas at Austin (http://ccvweb.csres.utexas.edu/software). The Carbo software is available for download with the open-source APBS software package at http://apbs.sf.net/.
机译：在本文中，我们提出了一种生物分子静电势的多分辨率比较方法，无需对生物分子进行整体结构比对。底层的计算几何算法使用多分辨率属性轮廓树（MACT）来比较体积标量场的拓扑特征。我们应用MACT来计算具有不同程度的序列，结构和功能相似性的大量蛋白质链的静电相似性度量。对于校准，我们还基于3D结构对齐和Carbo相似性指数分析，通过更传统的方法为这些链计算相似性度量。而且，由于MACT方法不依赖于成对的结构比对，因此其准确性和效率有望在未来跨结构多样蛋白的大规模分类工作中表现出色。 MACT方法以与Carbo相似性指数方法相当的水平区分蛋白质链。即，它能够准确地将蛋白质聚类为功能相关的基团，这些基团表现出对配体结合位点的强烈依赖性。可从链接的Web数据库http://ccvweb.cres.utexas.edu/MolSignature/和http://agave.wustl.edu/similarity/中获得分析结果。 MACT分析工具可从德克萨斯大学奥斯汀分校的计算可视化中心（http://ccvweb.csres.utexas.edu/software）作为拓扑分析和定量工具（TAQT）的公共领域库的一部分获得。 ）。可通过http://apbs.sf.net/上的开源APBS软件包下载Carbo软件。

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