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ARVO-CL: The OpenCL version of the ARVO package – An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Jan Busa Jr., Shura Hayryan, Ming-Chya Wu, Jan Busa, Chin-Kun Hu
Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
Computer Physics Communications, Volume 183, Issue 11, Pages 2494-2497, 2012

@article{buvsa2012arvo,

   title={ARVO-CL: The OpenCL version of the ARVO package–An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations},

   author={Bu{v{s}}a, J. and Hayryan, S. and Wu, M.C. and Hu, C.K.},

   journal={Computer Physics Communications},

   year={2012},

   publisher={Elsevier}

}

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Introduction of Graphical Processing Units (GPUs) and computing using GPUs in recent years opened possibilities for simple parallelization of programs. In this update, we present the modernized version of program ARVO [J. Busa, J. Dzurina, E. Hayryan, S. Hayryan, C.-K. Hu, J. Plavka, I. Pokorny, J. Skivanek, M.-C. Wu, Comput. Phys. Comm. 165 (2005) 59]. The whole package has been rewritten in the C language and parallelized using OpenCL. Some new tricks have been added to the algorithm in order to save memory much needed for efficient usage of graphical cards. A new tool called ‘input_structure" was added for conversion of pdb files into files suitable for work with the C and OpenCL version of ARVO.
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