Staff – Bioinformatics Centre - University of Copenhagen

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

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Lubomir Dimitrov Antonov, Christian Andreetta, Thomas Wim Hamelryck

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 languageEnglish
Title of host publicationBiomedical Engineering Systems and Technologies
EditorsJoaquim Gabriel, Jan Schier, Sabine Van Huffel
Number of pages14
Volume357
PublisherSpringer Science+Business Media
Publication date2013
Pages222-235
ISBN (Print)978-3-642-38255-0
ISBN (Electronic)978-3-642-38256-7
DOIs
Publication statusPublished - 2013
EventBIOSTEC 2012: International Joint Conference on Biomedical Engineering Systems and Technologies - Algarve, Portugal
Duration: 2 Feb 20125 Feb 2012
Conference number: 5

Conference

ConferenceBIOSTEC 2012
Nummer5
LandPortugal
ByAlgarve
Periode02/02/201205/02/2012
SeriesCommunications in Computer and Information Science
ISSN1865-0929

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