Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework

Lubomir Dimitrov Antonov; Christian Andreetta; Thomas Wim Hamelryck

doi:10.1007/978-3-642-38256-7_15

Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework

Lubomir Dimitrov Antonov, Christian Andreetta, Thomas Wim Hamelryck

Computational and RNA Biology

5 Citations (Scopus)

1635 Downloads (Pure)

Abstract

Inference of protein structure from experimental data is of crucial interest in science, medicine and biotechnology. Low-resolution methods, such as small angle X-ray scattering (SAXS), play a major role in investigating important biological questions regarding the structure of proteins in solution.
To infer protein structure from SAXS data, it is necessary to calculate the expected experimental observations given a protein structure, by making use of a so-called forward model. This calculation needs to be performed many times during a conformational search. Therefore, computational efficiency directly determines the complexity of the systems that can be explored.
We present an efficient implementation of the forward model for SAXS with full hardware utilization of Graphics Processor Units (GPUs). The proposed algorithm is orders of magnitude faster than an efficient CPU implementation, and implements a caching procedure employed in the partial forward model evaluations within a Markov chain Monte Carlo framework.

Original language	English
Title of host publication	Biomedical Engineering Systems and Technologies
Editors	Joaquim Gabriel, Jan Schier, Sabine Van Huffel
Number of pages	14
Volume	357
Publisher	Springer Science+Business Media
Publication date	2013
Pages	222-235
ISBN (Print)	978-3-642-38255-0
ISBN (Electronic)	978-3-642-38256-7
DOIs	https://doi.org/10.1007/978-3-642-38256-7_15
Publication status	Published - 2013
Event	BIOSTEC 2012: International Joint Conference on Biomedical Engineering Systems and Technologies - Algarve, Portugal Duration: 2 Feb 2012 → 5 Feb 2012 Conference number: 5

Conference

Conference	BIOSTEC 2012
Number	5
Country/Territory	Portugal
City	Algarve
Period	02/02/2012 → 05/02/2012

Series	Communications in Computer and Information Science
ISSN	1865-0929

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10.1007/978-3-642-38256-7_15

Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo FrameworkAccepted author manuscript, 1.63 MB

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Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework. / Antonov, Lubomir Dimitrov; Andreetta, Christian; Hamelryck, Thomas Wim.
Biomedical Engineering Systems and Technologies. ed. / Joaquim Gabriel; Jan Schier; Sabine Van Huffel. Vol. 357 Springer Science+Business Media, 2013. p. 222-235 (Communications in Computer and Information Science).

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

Antonov, LD, Andreetta, C & Hamelryck, TW 2013, Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework. in J Gabriel, J Schier & SV Huffel (eds), Biomedical Engineering Systems and Technologies. vol. 357, Springer Science+Business Media, Communications in Computer and Information Science, pp. 222-235, BIOSTEC 2012, Algarve, Portugal, 02/02/2012. https://doi.org/10.1007/978-3-642-38256-7_15

Antonov LD, Andreetta C, Hamelryck TW. Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework. In Gabriel J, Schier J, Huffel SV, editors, Biomedical Engineering Systems and Technologies. Vol. 357. Springer Science+Business Media. 2013. p. 222-235. (Communications in Computer and Information Science). doi: 10.1007/978-3-642-38256-7_15

Antonov, Lubomir Dimitrov ; Andreetta, Christian ; Hamelryck, Thomas Wim. / Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework. Biomedical Engineering Systems and Technologies. editor / Joaquim Gabriel ; Jan Schier ; Sabine Van Huffel. Vol. 357 Springer Science+Business Media, 2013. pp. 222-235 (Communications in Computer and Information Science).

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AB - Inference of protein structure from experimental data is of crucial interest in science, medicine and biotechnology. Low-resolution methods, such as small angle X-ray scattering (SAXS), play a major role in investigating important biological questions regarding the structure of proteins in solution.To infer protein structure from SAXS data, it is necessary to calculate the expected experimental observations given a protein structure, by making use of a so-called forward model. This calculation needs to be performed many times during a conformational search. Therefore, computational efficiency directly determines the complexity of the systems that can be explored.We present an efficient implementation of the forward model for SAXS with full hardware utilization of Graphics Processor Units (GPUs). The proposed algorithm is orders of magnitude faster than an efficient CPU implementation, and implements a caching procedure employed in the partial forward model evaluations within a Markov chain Monte Carlo framework.

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Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework

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