Parallel GPGPU Evaluation of Small Angle X-Ray Scattering Profiles in a Markov Chain Monte Carlo Framework
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.
KeywordsSAXS GPU GPGPU MCMC Protein Structure Determination OpenCL
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- 4.Hura, G.L., Menon, A.L., Hammel, M., Rambo, R.P., Poole, F.L., Tsutakawa, S.E., Jenney, F.E., Classen, S., Frankel, K.A., Hopkins, R.C., Jae Yang, S., Scott, J.W., Dillard, B.D., Adams, M.W.W., Tainer, J.A.: Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat. Methods 6, 606–614 (2009)CrossRefGoogle Scholar
- 17.Madl, T., Gabel, F., Sattler, M.: NMR and small-angle scattering-based structural analysis of protein complexes in solution. J. Struct. Biol., 1–11 (2010)Google Scholar
- 19.Stone, J.E., Gohara, D., Shi, G.: OpenCL: A parallel programming standard for heterogeneous computing systems. Computing in Science and Engineering 12, 66–73 (2010)Google Scholar
- 20.Schrödinger, L.: The PyMOL molecular graphics system, version 1.3r1 (2010)Google Scholar
- 23.Borg, M., Mardia, K., Boomsma, W., Frellsen, J., Harder, T., Stovgaard, K., Ferkinghoff-Borg, J., Røgen, P., Hamelryck, T.: A probabilistic approach to protein structure prediction: PHAISTOS in CASP9. In: Gusnanto, A., Mardia, K., Fallaize, C. (eds.) LASR2009 - Statistical Tools for Challenges in Bioinformatics, pp. 65–70. Leeds University Press, Leeds (2009)Google Scholar