-
2
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y., Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998, 282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
3
-
-
0037067120
-
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
-
Yeh I., Hummer G. Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J. Am. Chem. Soc. 2002, 124:6563-6568.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 6563-6568
-
-
Yeh, I.1
Hummer, G.2
-
4
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis J.L., Lindorff-Larsen K., Dror R.O., Shaw D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol. 2009, 19:120-127.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
5
-
-
27644502679
-
Simulating movement of tRNA into the ribosome during decoding
-
Sanbonmatsu K.Y., Joseph S., Tung C. Simulating movement of tRNA into the ribosome during decoding. Proc. Natl. Acad. Sci. USA 2005, 102:15854-15869.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15854-15869
-
-
Sanbonmatsu, K.Y.1
Joseph, S.2
Tung, C.3
-
6
-
-
33644848399
-
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
-
Freddolino P.L., Arkhipov A.S., Larson S.B., Mcpherson A., Schul-ten K. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 2006, 14:437-449.
-
(2006)
Structure
, vol.14
, pp. 437-449
-
-
Freddolino, P.L.1
Arkhipov, A.S.2
Larson, S.B.3
Mcpherson, A.4
Schul-ten, K.5
-
7
-
-
28144442197
-
A special purpose computer for molecular dynamics calculations
-
Bakker A.F., Gilmer G.H., Grabow M.H., Thompson K. A special purpose computer for molecular dynamics calculations. J. Comput. Phys. 1990, 90:313-335.
-
(1990)
J. Comput. Phys.
, vol.90
, pp. 313-335
-
-
Bakker, A.F.1
Gilmer, G.H.2
Grabow, M.H.3
Thompson, K.4
-
8
-
-
0026342528
-
FASTRUN: A special purpose, hardwired computer for molecular simulation
-
Fine R., Dimmler G., Levinthal C. FASTRUN: A special purpose, hardwired computer for molecular simulation. Protein Struct. Funct. Genet. 1991, 11:242-253.
-
(1991)
Protein Struct. Funct. Genet.
, vol.11
, pp. 242-253
-
-
Fine, R.1
Dimmler, G.2
Levinthal, C.3
-
9
-
-
0141754037
-
Hardware accelerator for molecular dynamics: MDGRAPE-2
-
Susukita R., Ebisuzaki T., Elmegreen B.G., Furusawa H., Kato K., Kawai A., Kobayashi Y., Koishi T., McNiven G.D., Narumi T., Yasuoka K. Hardware accelerator for molecular dynamics: MDGRAPE-2. Comput. Phys. Commun. 2003, 155:115-131.
-
(2003)
Comput. Phys. Commun.
, vol.155
, pp. 115-131
-
-
Susukita, R.1
Ebisuzaki, T.2
Elmegreen, B.G.3
Furusawa, H.4
Kato, K.5
Kawai, A.6
Kobayashi, Y.7
Koishi, T.8
McNiven, G.D.9
Narumi, T.10
Yasuoka, K.11
-
10
-
-
58049201323
-
-
University of California, San Francisco
-
Case D.A., Darden T.A., Cheatham T.E., Simmerling C.L., Wang J., Duke R.E., Luo R., Crowley M., Walker R.C., Zhang W., Merz K.M., Wang B., Hayik S., Roitberg A., Seabra G., Kolossvary I., Wong K.F., Paesani F., Vanicek J., Wu X., Brozell S.R., Steinbrecher T., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Mathews D.H., Seetin M.G., Sagui C., Babin V., Kollman P.A. AMBER 10 2008, University of California, San Francisco.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvary, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
11
-
-
23444454552
-
The amber biomolecular simulation programs
-
Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., Woods R.J. The amber biomolecular simulation programs. J. Comput. Chem. 2005, 26:1668-1688.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
12
-
-
70449466935
-
Performance analysis of clearspeed's CSX600 interconnects, in Parallel and Distributed Processing with Applications
-
Yuri N. Performance analysis of clearspeed's CSX600 interconnects, in Parallel and Distributed Processing with Applications. IEEE International Symposium 2009, 203-210.
-
(2009)
IEEE International Symposium
, pp. 203-210
-
-
Yuri, N.1
-
13
-
-
35348886062
-
Anton, a special-purpose machine for molecular dynamics simulation
-
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., Wang S.C. Anton, a special-purpose machine for molecular dynamics simulation. SIGARCH Comput. Archit. News 2007, 35:1-12.
-
(2007)
SIGARCH Comput. Archit. News
, vol.35
, pp. 1-12
-
-
Shaw, D.E.1
Deneroff, M.M.2
Dror, R.O.3
Kuskin, J.S.4
Larson, R.H.5
Salmon, J.K.6
Young, C.7
Batson, B.8
Bowers, K.J.9
Chao, J.C.10
Eastwood, M.P.11
Gagliardo, J.12
Grossman, J.P.13
Ho, R.C.14
Ierardi, D.J.15
Kolossváry, I.16
Klepeis, J.L.17
Layman, T.18
Mcleavey, C.19
Moraes, M.A.20
Mueller, R.21
Priest, E.C.22
Shan, Y.23
Spengler, J.24
Theobald, M.25
Towles, B.26
Wang, S.C.27
more..
-
14
-
-
77955767628
-
-
J. von Neumann Institute for Computing, Jülich, J. Meinke, O. Zimmermann, S. Mohanty, U.H.E. Hansmann (Eds.)
-
Narumi T., Ohno Y., Noriyuk F., Okimoto N., Suenaga A., Yanai R., Taiji M. From Computational Biophysics to Systems Biology: A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3 2006, 29-36. J. von Neumann Institute for Computing, Jülich. J. Meinke, O. Zimmermann, S. Mohanty, U.H.E. Hansmann (Eds.).
-
(2006)
From Computational Biophysics to Systems Biology: A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3
, pp. 29-36
-
-
Narumi, T.1
Ohno, Y.2
Noriyuk, F.3
Okimoto, N.4
Suenaga, A.5
Yanai, R.6
Taiji, M.7
-
15
-
-
77955723990
-
-
NVIDIA: Santa Clara, CA, CUDA Programming Guide (Accessed March 6, 2010)
-
NVIDIA: Santa Clara, CA, CUDA Programming Guide (Accessed March 6, 2010). http://deve-loper.download.nvidia.com/compute/cuda/30/toolkit/docs/NVIDIACU-DAProgrammingGuide3.0.pdf.
-
-
-
-
16
-
-
84864559630
-
First draft of a report on the EDVAC
-
von Neumann J. First draft of a report on the EDVAC. IEEE Ann. Hist. Comput. 1993, 15:27-75.
-
(1993)
IEEE Ann. Hist. Comput.
, vol.15
, pp. 27-75
-
-
von Neumann, J.1
-
17
-
-
0015401565
-
Some computer organizations and their effectiveness
-
Flynn M.J. Some computer organizations and their effectiveness. IEEE Trans. Comput. 1972, C-21:948-960.
-
(1972)
IEEE Trans. Comput.
, vol.21 C
, pp. 948-960
-
-
Flynn, M.J.1
-
19
-
-
33846339776
-
GPU accelerated molecular dynamics simulation of thermal conductivities
-
Yang J., Wang Y., Chen Y. GPU accelerated molecular dynamics simulation of thermal conductivities. J. Comput. Phys. 2007, 221:799-804.
-
(2007)
J. Comput. Phys.
, vol.221
, pp. 799-804
-
-
Yang, J.1
Wang, Y.2
Chen, Y.3
-
20
-
-
77955763824
-
-
AMD: Sunnyvale, CA, ATI, (Accessed March 14, 2010)
-
AMD: Sunnyvale, CA, ATI, (Accessed March 14, 2010). http://www.amd.com/stream.
-
-
-
-
21
-
-
0003651470
-
-
Addison-Wesley Longman Publishing Co., Inc, Boston, MA
-
Woo M., Neider J., Davis T., Shreiner D. OpenGL Programming Guide: The Official Guide to Learning OpenGL, version 1.2 1999, Addison-Wesley Longman Publishing Co., Inc, Boston, MA.
-
(1999)
OpenGL Programming Guide: The Official Guide to Learning OpenGL, version 1.2
-
-
Woo, M.1
Neider, J.2
Davis, T.3
Shreiner, D.4
-
22
-
-
38349105400
-
-
Springer, Berlin/Heidelberg, S. Aluru, M. Parashar, R. Badrinath, V.K. Prasanna (Eds.)
-
Liu W., Schmidt B., Voss G., Müller-Wittig W. High Performance Computing-HiPC 2007: Lecture Notes in Computer Science 2007, Vol. 4873:185-196. Springer, Berlin/Heidelberg. S. Aluru, M. Parashar, R. Badrinath, V.K. Prasanna (Eds.).
-
(2007)
High Performance Computing-HiPC 2007: Lecture Notes in Computer Science
, vol.4873
, pp. 185-196
-
-
Liu, W.1
Schmidt, B.2
Voss, G.3
Müller-Wittig, W.4
-
23
-
-
35948963714
-
Accelerating molecular modeling applications with graphics processors
-
Stone J.E., Phillips J.C., Freddolino P.L., Hardy D.J., Trabuco L.G., Schulten K. Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 2007, 28:2618-2640.
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 2618-2640
-
-
Stone, J.E.1
Phillips, J.C.2
Freddolino, P.L.3
Hardy, D.J.4
Trabuco, L.G.5
Schulten, K.6
-
24
-
-
70350754499
-
-
IEEE Press, Piscataway, NJ, USA
-
Phillips J.C., Stone J.E., Schulten K. Adapting a message-driven parallel application to gpu-accelerated clusters, In SC '08: Proceedings of the 2008 ACM/IEEE conference on Super computing, 1-9 2008, IEEE Press, Piscataway, NJ, USA.
-
(2008)
Adapting a message-driven parallel application to gpu-accelerated clusters, In SC '08: Proceedings of the 2008 ACM/IEEE conference on Super computing, 1-9
-
-
Phillips, J.C.1
Stone, J.E.2
Schulten, K.3
-
25
-
-
45849099839
-
Harvesting graphics power for MD simulations
-
van Meel J.A., Arnold A., Frenkel D., Portegies Zwart S.F., Belleman R.G. Harvesting graphics power for MD simulations. Mol. Simulat. 2008, 34:259-266.
-
(2008)
Mol. Simulat.
, vol.34
, pp. 259-266
-
-
van Meel, J.A.1
Arnold, A.2
Frenkel, D.3
Portegies Zwart, S.F.4
Belleman, R.G.5
-
27
-
-
41249087856
-
General purpose molecular dynamics simulations fully implemented on graphics processing units
-
Anderson J.A., Lorenz C.D., Travesset A. General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 2008, 227:5342-5359.
-
(2008)
J. Comput. Phys.
, vol.227
, pp. 5342-5359
-
-
Anderson, J.A.1
Lorenz, C.D.2
Travesset, A.3
-
28
-
-
77955722473
-
-
Springer, Berlin/Heidelberg
-
Davis J., Ozsoy A., Patel S., Taufer M. Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors 2009, Springer, Berlin/Heidelberg.
-
(2009)
Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors
-
-
Davis, J.1
Ozsoy, A.2
Patel, S.3
Taufer, M.4
-
29
-
-
67650099787
-
ACEMD: Accelerating biomolecular dynamics in the microsecond time scale
-
Harvey M.J., Giupponi G., De Fabritiis G. ACEMD: Accelerating biomolecular dynamics in the microsecond time scale. J. Chem. Theory Comput. 2009, 5:1632-1639.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1632-1639
-
-
Harvey, M.J.1
Giupponi, G.2
De Fabritiis, G.3
-
30
-
-
64649105762
-
Accelerating molecular dynamic simulation on graphics processing units
-
Friedrichs M.S., Eastman P., Vaidyanathan V., Houston M., Le Grand S., Beberg A.L., Ensign D.L., Bruns C.M., Pande V.S. Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem. 2009, 30:864-872.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 864-872
-
-
Friedrichs, M.S.1
Eastman, P.2
Vaidyanathan, V.3
Houston, M.4
Le Grand, S.5
Beberg, A.L.6
Ensign, D.L.7
Bruns, C.M.8
Pande, V.S.9
-
31
-
-
77955749642
-
-
University of California, San Francisco
-
Case D.A., Darden T.A., Cheatham T.E., Simmerling C.L., Wang J., Duke R.E., Luo R., Crowley M., Walker R.C., Williamson M.J., Zhang W., Merz K.M., Wang B., Hayik S., Roitberg A., Seabra G., Kolossváry I., Wong K.F., Paesani F., Vanicek J., Wu X., Brozell S.R., Steinbrecher T., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Mathews D.H., Seetin M.G., Sagui C., Babin V., Kollman P.A. Amber 11, Technical report 2010, University of California, San Francisco.
-
(2010)
Amber 11, Technical report
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Williamson, M.J.10
Zhang, W.11
Merz, K.M.12
Wang, B.13
Hayik, S.14
Roitberg, A.15
Seabra, G.16
Kolossváry, I.17
Wong, K.F.18
Paesani, F.19
Vanicek, J.20
Wu, X.21
Brozell, S.R.22
Steinbrecher, T.23
Gohlke, H.24
Yang, L.25
Tan, C.26
Mongan, J.27
Hornak, V.28
Cui, G.29
Mathews, D.H.30
Seetin, M.G.31
Sagui, C.32
Babin, V.33
Kollman, P.A.34
more..
-
32
-
-
33846823909
-
Particle mesh ewald: An Nlog(N) method for ewald sums in large systems
-
Darden T., York D., Pedersen L. Particle mesh ewald: An Nlog(N) method for ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
33
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103:8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
34
-
-
73349117827
-
An implementation of the smooth particle mesh Ewald method on GPU hardware
-
Harvey M.J., De Fabritiis G. An implementation of the smooth particle mesh Ewald method on GPU hardware. J. Chem. Theory Comput. 2009, 5:2371-2377.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2371-2377
-
-
Harvey, M.J.1
De Fabritiis, G.2
-
35
-
-
77950551363
-
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
-
Eastman P., Pande V.S. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 2010, 31:1268-1272.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1268-1272
-
-
Eastman, P.1
Pande, V.S.2
-
36
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 1983, 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
37
-
-
30744437399
-
Flexible simple point-charge water model with improved liquid-state properties
-
Wu Y., Tepper H.L., Voth G.A. Flexible simple point-charge water model with improved liquid-state properties. J. Chem. Phys. 2006, 124:24503.
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 24503
-
-
Wu, Y.1
Tepper, H.L.2
Voth, G.A.3
-
38
-
-
77955718885
-
-
(in preparation)
-
Grand S.L, Goetz A.W., Xu D., Poole D., Walker R.C. Accelerating of amber generalized born calculations using nvidia graphics processing units 2010, (in preparation).
-
(2010)
Accelerating of amber generalized born calculations using nvidia graphics processing units
-
-
Grand, S.L.1
Goetz, A.W.2
Xu, D.3
Poole, D.4
Walker, R.C.5
-
39
-
-
77955733021
-
-
(in preparation)
-
Grand S.L, Goetz A.W., Xu D., Poole D., Walker R.C. Achieving high performance in amber PME simulations using graphics processing units without compromising accuracy 2010, (in preparation).
-
(2010)
Achieving high performance in amber PME simulations using graphics processing units without compromising accuracy
-
-
Grand, S.L.1
Goetz, A.W.2
Xu, D.3
Poole, D.4
Walker, R.C.5
-
40
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26:1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
41
-
-
67649412164
-
The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations
-
Ensign D.L., Pande V.S. The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. Biophys. J. 2009, 96:L53-5.
-
(2009)
Biophys. J.
, vol.96
-
-
Ensign, D.L.1
Pande, V.S.2
-
42
-
-
76149136021
-
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
-
Voelz V.A., Bowman G.R., Beauchamp K., Pande V.S. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J. Am. Chem. Soc. 2010, 132:1526-1528.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 1526-1528
-
-
Voelz, V.A.1
Bowman, G.R.2
Beauchamp, K.3
Pande, V.S.4
-
43
-
-
0034623787
-
Computing: Screen savers of the world unite!
-
Shirts M., Pande V.S. Computing: Screen savers of the world unite!. Science 2000, 290:1903-1904.
-
(2000)
Science
, vol.290
, pp. 1903-1904
-
-
Shirts, M.1
Pande, V.S.2
-
44
-
-
77955723258
-
-
NVIDIA Corporation Next generation CUDA compute architecture: Fermi.
-
NVIDIA Corporation Next generation CUDA compute architecture: Fermi, 2009.
-
(2009)
-
-
|