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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

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

Weiya Chen¹, Chun Yao¹, Yingzhong Guo¹

¹School of Software Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.

BMC Bioinformatics

|September 30, 2020

Summary

This summary is machine-generated.

We developed pmTM-align, a parallel approach for protein structure alignment. This method significantly speeds up large-scale pairwise and multiple structure comparisons, improving efficiency for protein evolution and function studies.

Keywords:

Apache Spark Multiple structure alignment OpenMP Pairwise structure alignment

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Area of Science:

Computational biology
Structural bioinformatics
Bioinformatics

Background:

Protein structure comparison is crucial for understanding protein function and evolution.
The growing volume of protein structure data presents computational challenges for large-scale comparisons.
Existing methods like TM-align can be computationally intensive.

Purpose of the Study:

To develop a more efficient parallel approach for protein structure alignment.
To address the computational bottleneck in large-scale structure comparisons.
To improve the speed and scalability of pairwise and multiple structure alignment tasks.

Main Methods:

Proposed pmTM-align, a parallel protein structure alignment method based on mTM-align/TM-align.
Utilized Apache Spark for parallel pairwise structure alignments.
Employed OpenMP for phylogenetic tree-based multiple structure alignment on a single computer.

Main Results:

Parallelization and data structure optimization significantly accelerated mTM-align.
Spark-based alignments demonstrated near-ideal scalability for large datasets.
OpenMP accelerated multiple structure alignment and metric computation by 2-5 times.

Conclusions:

pmTM-align enables scalable computation for both pairwise and multiple protein structure alignments.
The tool provides more timely results for medium to large datasets compared to mTM-align.
Facilitates efficient analysis of large protein structure datasets.