High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies

Dmitry Suplatov; Yana Sharapova; Maxim Shegay; Nina Popova; Kateryna Fesko; Vladimir Voevodin; Vytas Švedas

doi:10.1007/978-3-030-36592-9_21

High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies

Dmitry Suplatov^*, Yana Sharapova, Maxim Shegay, Nina Popova, Kateryna Fesko, Vladimir Voevodin, Vytas Švedas

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

Abstract

Construction of a multiple alignment of proteins that implement different functions within a common structural fold of a superfamily is a valuable tool in bioinformatics, but represents a challenge. The process can be seen as a pipeline of independent sequential steps of an equivalent computational complexity each performed by a different set of algorithms. In this work the overall productivity of the corresponding Mustguseal protocol was significantly improved by selecting an appropriate optimization strategy for each step of the pipeline. This HPC-installation was used to collect and superimpose within 12 h a representative set of 299’976 sequences and structures of the fold-type I PLP-dependent enzymes what appears to be the largest alignment of a protein superfamily ever constructed. The use of hybrid acceleration strategies provided a routine access to a sequence/structure comparison of evolutionarily related proteins at a scale that would previously have been intractable to study the structure-function relationship and solve practically relevant problems, thus promoting the value of bioinformatics and HPC in protein engineering and drug discovery.

Original language	English
Title of host publication	Supercomputing - 5th Russian Supercomputing Days, RuSCDays 2019, Revised Selected Papers
Editors	Vladimir Voevodin, Sergey Sobolev
Publisher	Springer
Pages	249-264
Number of pages	16
ISBN (Print)	9783030365912
DOIs	https://doi.org/10.1007/978-3-030-36592-9_21
Publication status	Published - 1 Jan 2019
Event	5th Russian Supercomputing Days Conference, RuSCDays 2019 - Moscow, Russian Federation Duration: 23 Sept 2019 → 24 Sept 2019

Publication series

Name	Communications in Computer and Information Science
Volume	1129 CCIS
ISSN (Print)	1865-0929
ISSN (Electronic)	1865-0937

Conference

Conference	5th Russian Supercomputing Days Conference, RuSCDays 2019
Country/Territory	Russian Federation
City	Moscow
Period	23/09/19 → 24/09/19

Keywords

Bioinformatics
High-performance computing
Hybrid computing
Multiple alignment
Mustguseal
Protein superfamilies

ASJC Scopus subject areas

General Computer Science
General Mathematics

Fields of Expertise

Human- & Biotechnology

Access to Document

10.1007/978-3-030-36592-9_21

Cite this

Suplatov, D., Sharapova, Y., Shegay, M., Popova, N., Fesko, K., Voevodin, V., & Švedas, V. (2019). High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies. In V. Voevodin, & S. Sobolev (Eds.), Supercomputing - 5th Russian Supercomputing Days, RuSCDays 2019, Revised Selected Papers (pp. 249-264). (Communications in Computer and Information Science; Vol. 1129 CCIS). Springer. https://doi.org/10.1007/978-3-030-36592-9_21

High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies. / Suplatov, Dmitry; Sharapova, Yana; Shegay, Maxim et al.
Supercomputing - 5th Russian Supercomputing Days, RuSCDays 2019, Revised Selected Papers. ed. / Vladimir Voevodin; Sergey Sobolev. Springer, 2019. p. 249-264 (Communications in Computer and Information Science; Vol. 1129 CCIS).

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › peer-review

Suplatov, D, Sharapova, Y, Shegay, M, Popova, N, Fesko, K, Voevodin, V & Švedas, V 2019, High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies. in V Voevodin & S Sobolev (eds), Supercomputing - 5th Russian Supercomputing Days, RuSCDays 2019, Revised Selected Papers. Communications in Computer and Information Science, vol. 1129 CCIS, Springer, pp. 249-264, 5th Russian Supercomputing Days Conference, RuSCDays 2019, Moscow, Russian Federation, 23/09/19. https://doi.org/10.1007/978-3-030-36592-9_21

Suplatov D, Sharapova Y, Shegay M, Popova N, Fesko K, Voevodin V et al. High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies. In Voevodin V, Sobolev S, editors, Supercomputing - 5th Russian Supercomputing Days, RuSCDays 2019, Revised Selected Papers. Springer. 2019. p. 249-264. (Communications in Computer and Information Science). doi: 10.1007/978-3-030-36592-9_21

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High-Performance Hybrid Computing for Bioinformatic Analysis of Protein Superfamilies

Abstract

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