GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting
10.1039/c4fd00005f
Crossref journal-article
Royal Society of Chemistry (RSC)
Faraday Discuss. (292)
Abstract

Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithmsvis-à-visexisting tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.

Bibliography

Stone, J. E., McGreevy, R., Isralewitz, B., & Schulten, K. (2014). GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting. Faraday Discuss., 169, 265–283.

Authors 4
  1. John E. Stone (first)
  2. Ryan McGreevy (additional)
  3. Barry Isralewitz (additional)
  4. Klaus Schulten (additional)
References 60 Referenced 38
  1. 10.1038/nature12162 / Nature by Zhao (2013)
  2. 10.1038/nature08701 / Nature by Zhang (2010)
  3. 10.1016/j.str.2008.02.007 / Structure by Ludtke (2008)
  4. 10.1073/pnas.0711623105 / Proc. Natl. Acad. Sci. U. S. A. by Zhang (2008)
  5. 10.1038/nprot.2010.126 / Nat. Protoc. by Baker (2010)
  6. 10.1016/j.coviro.2011.05.019 / Curr. Opin. Virol. by Hryc (2011)
  7. 10.1038/emboj.2011.261 / EMBO J. by Zhang (2011)
  8. 10.1038/nsmb.1774 / Nat. Struct. Mol. Biol. by Maki-Yonekura (2010)
  9. 10.1016/j.jmb.2009.12.027 / J. Mol. Biol. by Cheng (2010)
  10. 10.1016/j.str.2005.01.007 / Structure by Fabiola (2005)
  11. 10.1107/S0907444900010908 / Acta Crystallogr., Sect. D: Biol. Crystallogr. by Roseman (2000)
  12. 10.1146/annurev.biochem.77.062906.171838 / Annu. Rev. Biochem. by Das (2008)
  13. 10.1016/j.str.2007.09.021 / Structure by Schröder (2007)
  14. 10.1529/biophysj.107.115949 / Biophys. J. by Jolley (2008)
  15. 10.1016/j.jsb.2004.03.002 / J. Struct. Biol. by Tama (2004)
  16. 10.1529/biophysj.108.139451 / Biophys. J. by Orzechowski (2008)
  17. 10.1016/j.jsb.2013.01.003 / J. Struct. Biol. by Chapman (2013)
  18. 10.1016/j.str.2007.11.016 / Structure by Topf (2008)
  19. 10.1016/j.str.2008.03.005 / Structure by Trabuco (2008)
  20. 10.1016/j.ymeth.2009.04.005 / Methods by Trabuco (2009)
  21. 10.1002/jcc.20289 / J. Comput. Chem. by Phillips (2005)
  22. 10.1063/1.2770738 / J. Chem. Phys. by Wells (2007)
  23. 10.1186/1471-2105-12-190 / BMC Bioinformatics by Schreiner (2011)
  24. 10.1016/j.str.2011.07.017 / Structure by Chan (2011)
  25. 10.1073/pnas.0811370106 / Proc. Natl. Acad. Sci. U. S. A. by Villa (2009)
  26. 10.1016/j.str.2009.09.010 / Structure by Gumbart (2009)
  27. 10.1126/science.1178535 / Science by Becker (2009)
  28. 10.1126/science.1177662 / Science by Seidelt (2009)
  29. 10.1016/j.jmb.2010.07.056 / J. Mol. Biol. by Trabuco (2010)
  30. J. Gumbart , E.Schreiner , L. G.Trabuco , K.-Y.Chan and K.Schulten , Molecular Machines in Biology , Cambridge University Press , 2011 , ch. 8, pp. 142–157 / Molecular Machines in Biology by Gumbart (2011)
  31. 10.1038/nsmb.2026 / Nat. Struct. Mol. Biol. by Frauenfeld (2011)
  32. 10.1038/emboj.2011.58 / EMBO J. by Agirrezabala (2011)
  33. 10.1002/prot.22976 / Proteins: Struct., Funct., Bioinf. by Li (2011)
  34. 10.1016/j.bpj.2009.04.031 / Biophys. J. by Hsin (2009)
  35. 10.1016/j.chemphys.2009.01.003 / Chem. Phys. by Sener (2009)
  36. 10.1016/j.jsb.2011.01.012 / J. Struct. Biol. by Vasishtan (2011)
  37. 10.1107/S0567739471000986 / Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. by Diamond (1971)
  38. 10.1107/S010876738400009X / Acta Crystallogr., Sect. A: Found. Crystallogr. by Jones (1984)
  39. 10.1002/j.1460-2075.1993.tb05919.x / EMBO J. by Stewart (1993)
  40. 10.1007/s12551-009-0026-3 / Biophys. Rev. by Wriggers (2010)
  41. 10.1107/S0907444911049791 / Acta Crystallogr., Sect. D: Biol. Crystallogr. by Wriggers (2012)
  42. 10.1002/jcc.20084 / J. Comput. Chem. by Pettersen (2004)
  43. 10.1006/jsbi.1999.4174 / J. Struct. Biol. by Ludtke (1999)
  44. 10.1107/S0108767394007130 / Acta Crystallogr., Sect. A: Found. Crystallogr. by Chapman (1995)
  45. 10.1006/jmbi.2002.5438 / J. Mol. Biol. by Chacón (2002)
  46. 10.1016/0263-7855(96)00018-5 / J. Mol. Graphics by Humphrey (1996)
  47. J. E. Stone , B.Isralewitz and K.Schulten , Proceedings of the XSEDE Extreme Scaling Workshop (XSW) , 2013 , pp. 4350 / Proceedings of the XSEDE Extreme Scaling Workshop (XSW) by Stone (2013)
  48. J. E. Stone , J.Gullingsrud , P.Grayson and K.Schulten , 2001 ACM Symposium on Interactive 3D Graphics , New York , 2001 , pp. 191–194 / 2001 ACM Symposium on Interactive 3D Graphics by Stone (2001)
  49. J. Frank , Three-dimensional electron microscopy of macromolecular assemblies , Oxford University Press , New York , 2006 (10.1093/acprof:oso/9780195182187.001.0001) / Three-dimensional electron microscopy of macromolecular assemblies by Frank (2006)
  50. 10.1145/363707.363723 / Commun. ACM by Kahan (1965)
  51. Y. He and C. H. Q.Ding , ICS '00: Proceedings of the 14th international conference on Supercomputing , New York, NY, USA , 2000 , pp. 225–234 / ICS '00: Proceedings of the 14th international conference on Supercomputing by He (2000)
  52. 10.1109/MCSE.2005.52 / Comput. Sci. Eng. by Bailey (2005)
  53. J. E. Stone , J.Saam , D. J.Hardy , K. L.Vandivort , W. W.Hwu and K.Schulten , Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units , ACM International Conference Proceeding Series , New York, NY, USA , 2009 , pp. 9–18 / Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units by Stone (2009)
  54. M. Krone , J. E.Stone , T.Ertl and K.Schulten , EuroVis - Short Papers 2012 , 2012 , pp. 67–71 / EuroVis - Short Papers 2012 by Krone (2012)
  55. 10.1002/jcc.23130 / J. Comput. Chem. by Roberts (2013)
  56. J. E. Stone , K. L.Vandivort and K.Schulten , Proceedings of the 8th International Workshop on Ultrascale Visualization , New York, NY, USA , 2013 , pp. 6:1–6:8 / Proceedings of the 8th International Workshop on Ultrascale Visualization by Stone (2013)
  57. 10.1145/1365490.1365500 / Queue by Nickolls (2008)
  58. 10.1006/jmbi.1993.1626 / J. Mol. Biol. by Sali (1993)
  59. 10.1371/journal.ppat.1003132 / PLoS Pathog. by Wang (2013)
  60. 10.1002/bip.22042 / Biopolymers by Chan (2012)
Dates
Type When
Created 11 years, 5 months ago (March 17, 2014, 8:30 a.m.)
Deposited 1 year, 4 months ago (April 17, 2024, 12:40 p.m.)
Indexed 1 month ago (July 19, 2025, 11:37 p.m.)
Issued 11 years, 7 months ago (Jan. 1, 2014)
Published 11 years, 7 months ago (Jan. 1, 2014)
Published Online 11 years, 7 months ago (Jan. 1, 2014)
Funders 0

None

@article{Stone_2014, title={GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting}, volume={169}, ISSN={1364-5498}, url={http://dx.doi.org/10.1039/c4fd00005f}, DOI={10.1039/c4fd00005f}, journal={Faraday Discuss.}, publisher={Royal Society of Chemistry (RSC)}, author={Stone, John E. and McGreevy, Ryan and Isralewitz, Barry and Schulten, Klaus}, year={2014}, pages={265–283} }