Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Journal of Molecular Graphics and Modelling

Volumn 28, Issue 8, 2010, Pages 904-910

  Anandakrishnan, Ramu ^a   Scogland, Tom R W ^a   Fenley, Andrew T ^b   Gordon, John C ^c   Feng, Wu chun ^b   Onufriev, Alexey V ^b  

^a Virginia Polytechnic Institute and State University   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^c MICROSOFT   (United States)

Author keywords

Biomolecular electrostatics; Graphical processing unit (GPU); Implicit solvent model; Multi scale modeling

Indexed keywords

BIO-MOLECULAR; BIOMOLECULAR ELECTROSTATICS; COARSE GRAINING; DESKTOP COMPUTER; ELECTROSTATIC POTENTIALS; ELECTROSTATIC SURFACES; GRAPHICAL PROCESSING UNITS; GRAPHICS PROCESSING UNIT; IMPLICIT SOLVENT MODEL; LARGE BIOMOLECULES; MULTI-SCALE MODELING; MULTIPLE PROCESSORS; MULTISCALE METHOD; MULTISCALES; PARALLEL IMPLEMENTATIONS; PARALLELIZATIONS; POISSON-BOLTZMANN; SPEED-UPS; TOOLS AND METHODS; VIRAL CAPSIDS;

DISSOCIATION; ELECTROSTATICS; IMAGE CODING; PROGRAM PROCESSORS; SPEED; SURFACE POTENTIAL; SURFACE PROPERTIES;

COMPUTER GRAPHICS EQUIPMENT;

CHAPERONIN; MYOGLOBIN; NITRITE REDUCTASE;

ACCURACY; ANALYTIC METHOD; ARTICLE; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER PROGRAM; CONTROLLED STUDY; INFORMATION PROCESSING; PRIORITY JOURNAL; STATIC ELECTRICITY; SURFACE PROPERTY; VIRUS CAPSID;

COMPUTATIONAL BIOLOGY; COMPUTERS; STATIC ELECTRICITY; SURFACE PROPERTIES;

MIRIDAE;

EID: 77951978448     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2010.04.001     Document Type: Article

References (57)

1. Perutz M. Electrostatic effects in proteins. Science 201 (1978) 1187-1191
2. Madura J.D., Davis M.E., Gilson M.K., Wade R.C., Luty B.A., Andrew J., and McCammon. Biological applications of electrostatic calculations and Brownian dynamics. Rev. Comp. Chem. 5 (1994) 229-267
3. Nicholls B.H.A. Classical electrostatics in biology and chemistry. Science 268 (1995) 1144-1149
4. Davis M.E., and Andrew McCammon J. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90 (1990) 509-521
5. Baker N.A., and McCammon J.A. Electrostaic Interactions In Structural Bioinformatics (2002), John Wiley & Sons, Inc, New York
6. Warshel A., and Åqvist J. Electrostatic energy and macromolecular function. Ann. Rev. Biophys. Biophys. Chem. 20 (1991) 267-298
7. Fersht A.R., Shi J.P., Knill-Jones J., Lowe D.M., Wilkinson A.J., Blow D.M., Brick P., Carter P., Waye M.M., and Winter G. Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314 (1985) 235-238
8. Szabo G., Eisenman G., McLaughlin S.G.A., and Krasne S. Ionic probes of membrane structures. Ann. N. Y. Acad. Sci. 195 (1972) 273-290 Membrane Structure and Its Biological Applications
9. Sheinerman F.B., Norel R., and Honig B. Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol 10 2 (2000) 153-159
10. Onufriev A., Smondyrev A., and Bashford D. Proton affinity changes during unidirectional proton transport in the bacteriorhodopsin photocycle. J. Mol. Biol. 332 (2003) 1183-1193
11. Yang A.-S., and Honig B. Electrostatic effects on protein stability. Curr. Opin. Struct. Biol. 2 (1992) 40-45
12. Whitten S., and Garcia-Moreno B. pH dependence of stability of staphyococcal nuclease: evidence of substantial electrostatic interactions in denatured state. Biochemistry 39 (2000) 14292-14304
13. Koehl P. Electrostatics calculations: latest methodological advances. Curr. Opin. Struct. Biol. 16 6 (2006) 142-151 March
14. Robertson A., Luttmann E., and Pande V.S. Effects of long-range electrostatic forces on simulated protein folding kinetics. J. Comput. Chem. 29 5 (2007) 694-700
15. Beck D.A.C., Armen R.S., and Daggett V. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry 44 2 (2005) 609-616 January
16. Ruvinsky A.M., and Vakser I.A. Interaction cutoff effect on ruggedness of protein-protein energy landscape. Proteins: Struct., Funct. Bioinform. 70 4 (2008) 1498-1505
17. Carrier J., Greengard L., and Rokhlin V. A fast adaptive multipole algorithm for particle simulations. SIAM J. Sci. Stat. Comput. 9 4 (1988) 669-686
18. Cai W., Deng S., and Jacobs D. Extending the fast multipole method to charges inside or outside a dielectric sphere. J. Comput. Phys. 223 May (2) (2007) 846-864
19. Lambert C.G., Darden T.A., and Board Jr. J.A. A multipole-based algorithm for efficient calculation of forces and potentials in macroscopic periodic assemblies of particles. J. Comput. Phys. 126 July (2) (1996) 274-285
20. Darden T., York D., and Pedersen L. Particle mesh Ewald: An N. log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 12 (1993) 10089-10092
21. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103 19 (1995) 8577-8593
22. Toukmaji A.Y., and Board J.A. Ewald summation techniques in perspective: a survey. Comp. Phys. Commun. 95 June (2-3) (1996) 73-92
23. York D., and Yang W. The fast fourier Poisson method for calculating Ewald sums. J. Chem. Phys. 101 4 (1994) 3298-3300
24. Schlick T. Molecular Modeling and Simulation, An Interdisciplinary Guide (2002), Springer-Verlag, New York
25. Anandakrishnan R., and Onufriev A.V. An n log n approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. J. Comput. Chem. 31 4 (2010) 691-706
26. Onufriev A. Implicit solvent models in molecular dynamics simulations. Annu. Rep. Comput. Chem. 4 (2008) 125-137
27. Los Alamos National Laboratory. mpiBLAST. http://mpiblast.lanl.gov/.
28. Konecny R., Trylska J., Tama F., Zhang D., Baker N.A., Brooks C.L., and McCammon J.A. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 82 June (2) (2006) 106-120
29. Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U.S.A. 98 August (18) (2001) 10037-10041
30. Klepeis J.L., Lindorff-Larsen K., Dror R.O., and Shaw D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol. 19 April (2) (2009) 120-127
31. Ruscio J.Z., Kumar D., Shukla M., Prisant M.G., Murali T.M., and Onufriev A.V. Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin. Proc. Natl. Acad. Sci. U.S.A. 105 27 (2008) 9204-9209
32. Kumar S., Huang C., Zheng G., Bohm E., Bhatele A., Phillips J.C., Yu H., and Kalé L.V. Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. IBM J. Res. Dev. 52 1/2 (2008) 177-187
33. Shaw D.E., Deneroff M.M., Dror R.O., Kuskin J.S., Larson R.H., Salmon J.K., Young C., Batson B., Bowers K.J., Chao J.C., Eastwood M.P., Gagliardo J., Grossman J.P., Ho R.C., Ierardi D.J., Kolossváry I., Klepeis J.L., Layman T., Mcleavey C., Moraes M.A., Mueller R., Priest E.C., Shan Y., Spengler J., Theobald M., Towles B., and Wang S.C. Anton a special-purpose machine for molecular dynamics simulation. Commun. ACM 51 7 (2008) 91-97
34. Zhou R., Eleftheriou M., Hon C.C., Germain R.S., Royyuru A.K., and Berne B.J. Massively parallel molecular dynamics simulations of lysozyme unfolding. IBM J. Res. Dev. 52 1/2 (2008) 19
35. Moore G. Cramming more components onto integrated circuits. Electron. Mag. April (1965)
36. Sriram Swaminarayan., Kai Kadau., Timothy C.Germann., and Gordon C. Fossum 369 tflop/s molecular dynamics simulations on the roadrunner general-purpose heterogeneous supercomputer. SC'08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing (2008), IEEE Press, Piscataway, NJ, USA 1-10
37. Archuleta J., Cao Y., Feng W., and Scogland T. Multi-dimensional characterization of temporal data mining on graphics processors. 23rd IEEE International Parallel and Distributed Processing Symposium, May (2009)
38. Dynerman D., Butzlaff E., and Mitchell J.C. CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation. J. Comput. Biol. 16 4 (2009) 523-537
39. Narumi T., Yasuoka K., Taiji M., and Höfinger S. Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach. J. Comput. Chem. 30 14 (2009) 2351-2357
40. Ufimtsev I.S., and Martinez T.J. Quantum chemistry on graphical processing units. 1. Strategies for two-electron integral evaluation. J. Chem. Theory Comput. 4 February (2) (2008) 222-231
41. Anderson J.A., Lorenz C.D., and Travesset A. General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 227 10 (2008) 5342-5359
42. Friedrichs M.S., Eastman P., Vaidyanathan V., Houston M., Legrand S., Beberg A.L., Ensign D.L., Bruns C.M., and Pande V.S. Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem. 30 6 (2009) 864-872
43. Hardy D.J., Stone J.E., and Schulten K. Multilevel summation of electrostatic potentials using graphics processing units. Parallel Comput. 35 3 (2009) 164-177
44. Stone J.E., Phillips J.C., Freddolino P.L., Hardy D.J., Trabuco L.G., and Schulten K. Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28 16 (2007) 2618-2640
45. Gordon J.C., Fenley A.T., and Onufriev A. An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications. J. Chem. Phys. 129 7 (2008) 075102
46. Sigalov G., Fenley A., and Onufriev A. Analytical linearized Poisson-Boltzmann approach: Beyond the generalized Born approximation. J. Chem. Phys. 124 (2006) 124902
47. Fenley A.T., Gordon J.C., and Onufriev A. An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis. J. Chem. Phys. 129 7 (2008) 075101
48. Sigalov G., Scheffel P., and Onufriev A. Incorporating variable dielectric environments into the generalized born model. J. Chem. Phys. 122 Mar (9) (2005) 094511-194511
49. AMD/ATI Brook+. http://sourceforge.net/projects/brookplus/. 2000.
50. Buck I., Foley T., Horn D., Sugerman J., Fatahalian K., Houston M., and Hanrahan P. Brook for GPUs: stream computing on graphics hardware. ACM Trans. Graph. 23 3 (2004) 777-786
51. Advanced Micro Devices ATI Stream Computing User Guide, March 2009.
52. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
53. Gordon J.C., Myers J.B., Folta T., Shoja V., Heath L.S., and Onufriev A.L. H++: a server for estimating pKa's and adding missing hydrogens to macromolecules. Nucleic Acids Res. 33 (2005) 68-71
54. Bashford D., and Gerwert K. Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J. Mol. Biol. 224 (1992) 473-486
55. Sanner M.F., Olson A.J., Claude J., and Spehner. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38 3 (1996) 305-320
56. Abagyan R. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5 August (4) (2001) 375-382
57. Teodoro M.L., Phillips G.N., and Kavraki Jr. L.E. Molecular docking: a problem with thousands of degrees of freedom. In IEEE International Conference on Robotics and Automation (2001) 960-966