Department of Computer Science, University of Pisa Pisa, Italy.
Department of Clinical and Molecular Biomedicine, University of Catania Catania, Italy.
Front Genet. 2014 Sep 2;5:302. doi: 10.3389/fgene.2014.00302. eCollection 2014.
Multiple local structure comparison helps to identify common structural motifs or conserved binding sites in 3D structures in distantly related proteins. Since there is no best way to compare structures and evaluate the alignment, a wide variety of techniques and different similarity scoring schemes have been proposed. Existing algorithms usually compute the best superposition of two structures or attempt to solve it as an optimization problem in a simpler setting (e.g., considering contact maps or distance matrices). Here, we present PROPOSAL (PROteins comparison through Probabilistic Optimal Structure local ALignment), a stochastic algorithm based on iterative sampling for multiple local alignment of protein structures. Our method can efficiently find conserved motifs across a set of protein structures. Only the distances between all pairs of residues in the structures are computed. To show the accuracy and the effectiveness of PROPOSAL we tested it on a few families of protein structures. We also compared PROPOSAL with two state-of-the-art tools for pairwise local alignment on a dataset of manually annotated motifs. PROPOSAL is available as a Java 2D standalone application or a command line program at http://ferrolab.dmi.unict.it/proposal/proposal.html.
多区域结构比对有助于识别远距离相关蛋白质 3D 结构中的共同结构基序或保守结合位点。由于没有比较结构和评估比对的最佳方法，因此已经提出了各种各样的技术和不同的相似度评分方案。现有的算法通常计算两个结构的最佳叠加，或者尝试将其作为更简单设置（例如，考虑接触图或距离矩阵）中的优化问题来解决。在这里，我们提出了 PROPOSAL（通过概率最优结构局部比对进行蛋白质比较），这是一种基于迭代采样的随机算法，用于蛋白质结构的多个局部比对。我们的方法可以有效地在一组蛋白质结构中找到保守的模体。只计算结构中所有残基对之间的距离。为了展示 PROPOSAL 的准确性和有效性，我们在一些蛋白质结构家族上对其进行了测试。我们还将 PROPOSAL 与两个最先进的用于手动注释模体数据集的成对局部比对工具进行了比较。PROPOSAL 可作为 Java 2D 独立应用程序或命令行程序在 http://ferrolab.dmi.unict.it/proposal/proposal.html 上获得。
