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parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systemsстатья
Статья опубликована в высокорейтинговом журнале
Статья опубликована в журнале из списка Web of Science и/или Scopus- Авторы: Shegay Maksim V., Suplatov Dmitry A., Popova Nina N., Švedas Vytas K., Voevodin Vladimir V.
- Журнал: Bioinformatics
- Год издания: 2019
- Издательство: Oxford University Press
- Местоположение издательства: United Kingdom
- DOI: 10.1093/bioinformatics/btz224
- Аннотация: Motivation Accurate structural alignment of proteins is crucial at studying structure-function relationship in evolutionarily distant homologues. Various software tools were proposed to align multiple protein 3D-structures utilizing one CPU and thus are of limited productivity at large-scale analysis of protein families/superfamilies. Results The parMATT is a hybrid MPI/pthreads/OpenMP parallel re-implementation of the MATT algorithm to align multiple protein 3D-structures by allowing translations and twists. The parMATT can be faster than MATT on a single multi-core CPU, and provides a much greater speedup when executed on distributed-memory systems, i.e., computing clusters and supercomputers hosting memory-independent computing nodes. The most computationally demanding steps of the MATT algorithm — the initial construction of pairwise alignments between all input structures and further iterative progression of the multiple alignment — were parallelized using MPI and pthreads, and the concluding refinement step was optimized by introducing the OpenMP support. The parMATT can significantly accelerate the time-consuming process of building a multiple structural alignment from a large set of 3D-records of homologous proteins. Availability The source code is available at https://biokinet.belozersky.msu.ru/parMATT
- Добавил в систему: Суплатов Дмитрий Андреевич