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

Publikation: Bidrag til bog/antologi/rapportBidrag til bog/antologiForskningfagfællebedømt

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.
OriginalsprogEngelsk
TitelBiomedical Engineering Systems and Technologies
RedaktørerJoaquim Gabriel, Jan Schier, Sabine Van Huffel
Antal sider14
Vol/bind357
ForlagSpringer Science+Business Media
Publikationsdato2013
Sider222-235
ISBN (Trykt)978-3-642-38255-0
ISBN (Elektronisk)978-3-642-38256-7
DOI
StatusUdgivet - 2013
BegivenhedBIOSTEC 2012: International Joint Conference on Biomedical Engineering Systems and Technologies - Algarve, Portugal
Varighed: 2 feb. 20125 feb. 2012
Konferencens nummer: 5

Konference

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

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