Structure comparison can provide useful information to identify functional and evolutionary relationship between proteins. With the dramatic increase of protein structure data in the Protein Data Bank, computation time quickly becomes the bottleneck for large scale structure comparisons. To more efficiently deal with informative multiple structure alignment tasks, we propose pmTM-align, a parallel protein structure alignment approach based on mTM-align/TM-align. pmTM-align contains two stages to handle pairwise structure alignments with Spark and the phylogenetic tree-based multiple structure alignment task on a single computer with OpenMP. Experiments with the SABmark dataset showed that parallelization along with data structure optimization provided considerable speedup for mTM-align. The Spark-based structure alignments achieved near ideal scalability with large datasets, and the OpenMP-based construction of the phylogenetic tree accelerated the incremental alignment of multiple structures and metrics computation by a factor of about 2–5. pmTM-align enables scalable pairwise and multiple structure alignment computing and offers more timely responses for medium to large-sized input data than existing alignment tools such as mTM-align.

中文翻译：

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pmTM-align：使用Apache Spark和OpenMP可扩展的成对和多结构对齐

结构比较可以提供有用的信息，以鉴定蛋白质之间的功能和进化关系。随着蛋白质数据库中蛋白质结构数据的急剧增加，计算时间迅速成为大规模结构比较的瓶颈。为了更有效地处理信息丰富的多结构比对任务，我们提出了pmTM-align，这是一种基于mTM-align / TM-align的并行蛋白质结构比对方法。pmTM-align包含两个阶段，可在带有OpenMP的单台计算机上处​​理Spark的成对结构比对以及基于系统树的系统进化树多结构比对任务。SABmark数据集的实验表明，并行化与数据结构优化一起为mTM对齐提供了可观的加速。基于Spark的结构比对可通过大型数据集实现接近理想的可伸缩性，基于OpenMP的系统树的构建将多个结构和度量计算的增量比对加快了约2-3倍。与现有的对齐工具（如mTM-align）相比，pmTM-align支持可扩展的成对和多结构对齐计算，并且对中大型输入数据提供更及时的响应。