pmTM‑align: scalable pairwise and multiple structure alignment with Apache Spark and OpenMP

Weiya Chen, Chun Yao, Yingzhong Guo, Yan Wang, Zhidong Xue

Abstract

Background: 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 efciently 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.

Results: Experiments with the SABmark dataset showed that parallelization along with data structure optimization provided considerable speedup for mTM-align. The Sparkbased 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.

Conclusions: pmTM-align enables scalable pairwise and multiple structure alignment computing and ofers more timely responses for medium to large-sized input data than existing alignment tools such as mTM-align.

Keywords: Pairwise structure alignment, Multiple structure alignment, Apache Spark, OpenMP

https://doi.org/10.1186/s12859-020-03757-2