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Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler
Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on

@conference{lowe2011poster,

   title={Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps},

   author={Lowe, E.W. and Woetzel, N. and Meiler, J.},

   booktitle={Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on},

   pages={265–265},

   organization={IEEE}

}

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Three initial fits of 1ubi in a 6.6A resolution synthesized density map had backbone RMSDs to the correct placement of 2.7, 2.9 and 6.6A. They have been refined with a Powell optimizer [5] in 10 iterations using 6 directions, 3 rotations a, beta with 0.15 radians and gamma with 0.075 radians starting direction to cover the entire euler sphere and translation with 1.1A search directions in x, y and z. Each line search was terminated after 10 iterations or if dCCC lg 0.001. TABLE I. summarizes timings on CPU and 4 different GPU architectures in double floating point precision.
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