Lubomir D. Antonov, Christian Andreetta, Thomas Hamelryck


The inference of protein structure from experimental data is of crucial interest in science, medicine and biotechnology. Unfortunately, high-resolution experimental methods can not yet provide a detailed analysis of the ensemble of conformations adopted under physiological conditions. Low resolution techniques are often better suited for this task. Small angle X-ray scattering (SAXS) plays a major role in investigating important biological questions regarding the structure of multidomain proteins connected by flexible linkers or the aggregation processes that underlie several major diseases in humans. In silico simulations can bridge the gap between low resolution information and models derived from highresolution techniques. For that, it is necessary to be able to calculate the low resolution information from a given detailed model using a so-called forward model. These calculations need to be performed many times during a conformational search, and therefore need to be computationally efficient. We present an efficient implementation of the forward model for SAXS experiments with full hardware utilization of General Purpose Graphical Processor Units (GPGPUs). The proposed algorithm is orders of magnitude faster than an efficient CPU implementation, and implements a caching procedure ready to be employed in the partial SAXS evaluations required by in silico simulations.


  1. Anfinsen, C. B. (1973). Principles that govern the folding of protein chains. Science, 181(96):223-230.
  2. Boomsma, W., Mardia, K., Taylor, C., Ferkinghoff-Borg, J., Krogh, A., and Hamelryck, T. (2008). A generative, probabilistic model of local protein structure. Proc Natl Acad Sci U S A, 105(26):8932-8937.
  3. Chacon, P., Moran, F., Diaz, J., Pantos, E., and Andreu, J. (1998). Low-resolution structures of proteins in solution retrieved from x-ray scattering with a genetic algorithm. Biophys J, 74:2760-2775.
  4. Debye, P. (1915). Zerstreuung von rontgenstrahlen. Ann Phys, 351(6):809-823.
  5. Förster, F., Webb, B., Krukenberg, K., and Tsuruta, H. (2008). Integration of small-angle x-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol, 382:1089-1106.
  6. Franke, D. and Svergun, D. I. (2009). Dammif, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Crystallogr, 42(2):342-346.
  7. Göddeke, D. and Strzodka, R. a. (2011). Cyclic reduction tridiagonal solvers on GPUs applied to mixed precision multigrid. IEEE Transactions on Parallel and Distributed Systems, 22(1):22-32. doi: 10.1109/TPDS.2010.61.
  8. Habeck, M., Rieping, W., and Nilges, M. (2006). Weighting of experimental evidence in macromolecular structure determination. Proc Natl Acad Sci U S A, 103(6):1756-1761.
  9. Harder, T., Boomsma, W., Paluszewski, M., Frellsen, J., Johansson, K. E., and Hamelryck, T. (2010). Beyond rotamers: a generative, probabilistic model of side chains in proteins. BMC Bioinformatics, 11:306.
  10. Higham, N. J. (1993). The accuracy of floating point summation. SIAM J. Sci. Comput, 14:783-799.
  11. 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., and Tainer, J. A. (2009). Robust, high-throughput solution structural analyses by small angle x-ray scattering (saxs). Nat Methods, 6(8):606-614.
  12. Koch, M., Vachette, P., and Svergun, D. (2003). Smallangle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys, 36(2):147-227.
  13. Levitt, M. (2009). Nature of the protein universe. Proc Natl Acad Sci U S A, 106(27):11079-11084.
  14. Madl, T., Gabel, F., and Sattler, M. (2010). NMR and smallangle scattering-based structural analysis of protein complexes in solution. J Struct Biol, pages 1-11.
  15. Schrödinger, L. (2010). The PyMOL molecular graphics system, version 1.3r1.
  16. Stone, J. E., Gohara, D., and Shi, G. (2010). Opencl: A parallel programming standard for heterogeneous computing systems. Computing in Science and Engineering, 12:66-73.
  17. Stovgaard, K., Andreetta, C., Ferkinghoff-Borg, J., and Hamelryck, T. (2010). Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. BMC Bioinformatics, 11:429.
  18. Svergun, D. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J, 76:2879-2886.
  19. Svergun, D., Barberato, C., and Koch, M. (1995). Crysol - a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr, 28:768-773.
  20. Svergun, D., Petoukhov, M., and Koch, M. (2001). Determination of domain structure of proteins from x-ray solution scattering. Biophys J, 80(6):2946-2953.
  21. Svergun, D. I. and Stuhrmann, H. B. (1991). New developments in direct shape determination from small-angle scattering. 1. theory and model calculations. Acta Crystallogr A, 47(6):736-744.
  22. Tjioe, E. and Heller, W. (2007). Ornl sas: software for calculation of small-angle scattering intensities of proteins and protein complexes. J Appl Crystallogr, 40:782-785.
  23. Toft, K., Vestergaard, B., Nielsen, S., and Snakenborg, D. (2008). High-throughput small angle x-ray scattering from proteins in solution using a microfluidic frontend. Anal Chem, 80(10):3648-3654.
  24. Zheng, W. and Doniach, S. (2005). Fold recognition aided by constraints from small angle x-ray scattering data. Protein Eng Des Sel, 18(5):209-219.

Paper Citation

in Harvard Style

D. Antonov L., Andreetta C. and Hamelryck T. (2012). AN EFFICIENT PARALLEL GPU EVALUATION OF SMALL ANGLE X-RAY SCATTERING PROFILES . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 102-108. DOI: 10.5220/0003781501020108

in Bibtex Style

author={Lubomir D. Antonov and Christian Andreetta and Thomas Hamelryck},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},

in EndNote Style

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
SN - 978-989-8425-90-4
AU - D. Antonov L.
AU - Andreetta C.
AU - Hamelryck T.
PY - 2012
SP - 102
EP - 108
DO - 10.5220/0003781501020108