8859

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

Lubomir D. Antonov, Christian Andreetta, Thomas Hamelryck
The Bioinformatics Section, Department of Biology, University of Copenhagen, Denmark
University of Copenhagen, 2013
@article{antonov2013parallel,

   title={Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework},

   author={Antonov, L.D. and Andreetta, C. and Hamelryck, T.},

   year={2013}

}

Download Download (PDF)   View View   Source Source   Source codes Source codes

Package:

1015

views

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.
VN:F [1.9.22_1171]
Rating: 4.5/5 (2 votes cast)
Parallel GPGPU Evaluation of Small Angle X-ray Scattering Profiles in a Markov Chain Monte Carlo Framework, 4.5 out of 5 based on 2 ratings

* * *

* * *

TwitterAPIExchange Object
(
    [oauth_access_token:TwitterAPIExchange:private] => 301967669-yDz6MrfyJFFsH1DVvrw5Xb9phx2d0DSOFuLehBGh
    [oauth_access_token_secret:TwitterAPIExchange:private] => o29ji3VLVmB6jASMqY8G7QZDCrdFmoTvCDNNUlb7s
    [consumer_key:TwitterAPIExchange:private] => TdQb63pho0ak9VevwMWpEgXAE
    [consumer_secret:TwitterAPIExchange:private] => Uq4rWz7nUnH1y6ab6uQ9xMk0KLcDrmckneEMdlq6G5E0jlQCFx
    [postfields:TwitterAPIExchange:private] => 
    [getfield:TwitterAPIExchange:private] => ?cursor=-1&screen_name=hgpu&skip_status=true&include_user_entities=false
    [oauth:protected] => Array
        (
            [oauth_consumer_key] => TdQb63pho0ak9VevwMWpEgXAE
            [oauth_nonce] => 1472416538
            [oauth_signature_method] => HMAC-SHA1
            [oauth_token] => 301967669-yDz6MrfyJFFsH1DVvrw5Xb9phx2d0DSOFuLehBGh
            [oauth_timestamp] => 1472416538
            [oauth_version] => 1.0
            [cursor] => -1
            [screen_name] => hgpu
            [skip_status] => true
            [include_user_entities] => false
            [oauth_signature] => J5pPDmJ9dcxrk10aAbd2esJDF/c=
        )

    [url] => https://api.twitter.com/1.1/users/show.json
)
Follow us on Facebook
Follow us on Twitter

HGPU group

1969 peoples are following HGPU @twitter

HGPU group © 2010-2016 hgpu.org

All rights belong to the respective authors

Contact us: