-
1
-
-
0018793861
-
-
Frauenfelder, H.; Petsko, G. A.; Tsernoglou, D. Nature 1979, 280, 558-563
-
(1979)
Nature
, vol.280
, pp. 558-563
-
-
Frauenfelder, H.1
Petsko, G.A.2
Tsernoglou, D.3
-
2
-
-
0023746244
-
-
Frauenfelder, H.; Parak, F.; Young, R. D. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 451-479
-
(1988)
Annu. Rev. Biophys. Biophys. Chem.
, vol.17
, pp. 451-479
-
-
Frauenfelder, H.1
Parak, F.2
Young, R.D.3
-
4
-
-
70350340728
-
-
Boehr, D. D.; Nussinov, R.; Wright, P. E. Nat. Chem. Biol. 2009, 5, 789-796
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
5
-
-
71449103005
-
-
Fraser, J.; Clarkson, M.; Degnan, S.; Erion, R.; Kern, D.; Alber, T. Nature 2009, 462, 669-673
-
(2009)
Nature
, vol.462
, pp. 669-673
-
-
Fraser, J.1
Clarkson, M.2
Degnan, S.3
Erion, R.4
Kern, D.5
Alber, T.6
-
6
-
-
33748781457
-
-
Boehr, D. D.; Dyson, H. J.; Wright, P. E. Science 2006, 313, 1638-1642
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
Dyson, H.J.2
Wright, P.E.3
-
7
-
-
0034595671
-
-
Zaccai, G. Science 2000, 288, 1604-1607
-
(2000)
Science
, vol.288
, pp. 1604-1607
-
-
Zaccai, G.1
-
9
-
-
0037154884
-
-
Eisenmesser, E. Z.; Bosco, D. A.; Akke, M.; Kern, D. Science 2002, 295, 1520-1523
-
(2002)
Science
, vol.295
, pp. 1520-1523
-
-
Eisenmesser, E.Z.1
Bosco, D.A.2
Akke, M.3
Kern, D.4
-
10
-
-
27744499156
-
-
Eisenmesser, E. Z.; Millet, O.; Labeikovsky, W.; Korzhnev, D.; Bosco, D.; Skalicky, J.; Kay, L.; Kern, D. Nature 2005, 438, 117-121
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.4
Bosco, D.5
Skalicky, J.6
Kay, L.7
Kern, D.8
-
11
-
-
0029123975
-
-
Balbach, J.; Forge, V.; van Nuland, N. A. J.; Winder, S. L.; Hore, P. J.; Dobson, C. M. Nat. Struct. Mol. Biol. 1995, 2, 865-870
-
(1995)
Nat. Struct. Mol. Biol.
, vol.2
, pp. 865-870
-
-
Balbach, J.1
Forge, V.2
Van Nuland, N.A.J.3
Winder, S.L.4
Hore, P.J.5
Dobson, C.M.6
-
14
-
-
35948963714
-
-
Stone, J. E.; Phillips, J.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L.; Schulten, K. J. Comput. Chem. 2007, 28, 2618-2640
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 2618-2640
-
-
Stone, J.E.1
Phillips, J.2
Freddolino, P.L.3
Hardy, D.J.4
Trabuco, L.5
Schulten, K.6
-
15
-
-
41249087856
-
-
Anderson, J. A.; Lorenz, C. D.; Travesset, A. 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
-
16
-
-
64649105762
-
-
Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; LeGrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. 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
Legrand, S.5
Beberg, A.L.6
Ensign, D.L.7
Bruns, C.M.8
Pande, V.S.9
-
17
-
-
77956962231
-
-
Towards In;;, Smari, W. A.; McIntire, J. P., Eds.; HPCS' 10; IEEE: Piscataway, NJ
-
Hampton, S.; Agarwal, P. K.; Alam, S. R.; Crozier, P. S. Towards In Proceedings of the International Conference on High Performance Computing & Simulation; Smari, W. A.; McIntire, J. P., Eds.; HPCS' 10; IEEE: Piscataway, NJ, 2010; pp 98-107.
-
(2010)
Proceedings of the International Conference on High Performance Computing & Simulation
, pp. 98-107
-
-
Hampton, S.1
Agarwal, P.K.2
Alam, S.R.3
Crozier, P.S.4
-
18
-
-
33846148305
-
-
Bowers, K. J.; Dror, R. O.; Shaw, D. E. J. Comput. Phys. 2007, 221, 303-329
-
(2007)
J. Comput. Phys.
, vol.221
, pp. 303-329
-
-
Bowers, K.J.1
Dror, R.O.2
Shaw, D.E.3
-
19
-
-
46249092554
-
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
20
-
-
0003946510
-
-
2 nd ed.; Springer-Verlag New York, Inc.: New York,; Springer Series in Statistics.
-
Jolliffe, I. T. Principal Component Analysis, 2 nd ed.; Springer-Verlag New York, Inc.: New York, 2002; Springer Series in Statistics.
-
(2002)
Principal Component Analysis
-
-
Jolliffe, I.T.1
-
22
-
-
0027441950
-
-
Amadei, A.; Lissen, A. B. M.; Berendsen, H. J. C. Proteins 1993, 17, 412-425
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Lissen, A.B.M.2
Berendsen, H.J.C.3
-
23
-
-
49449086650
-
-
Materese, C. K.; Goldmon, C. C.; Papoian, G. A. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 10659-10664
-
(2008)
Proc. Natl. Acad. Sci. U. S. A.
, vol.105
, pp. 10659-10664
-
-
Materese, C.K.1
Goldmon, C.C.2
Papoian, G.A.3
-
26
-
-
70349631761
-
-
Bowman, G. R.; Beauchamp, K. A.; Boxer, G.; Pande, V. S. J. Chem. Phys. 2009, 131, 124101
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 124101
-
-
Bowman, G.R.1
Beauchamp, K.A.2
Boxer, G.3
Pande, V.S.4
-
27
-
-
36649006642
-
-
Shao, J.; Tanner, S.; Thompson, N.; Cheatham, T. J. Chem. Theory Comput. 2007, 3, 2312-2334
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2312-2334
-
-
Shao, J.1
Tanner, S.2
Thompson, N.3
Cheatham, T.4
-
28
-
-
59849098285
-
-
Frickenhaus, S.; Kannan, S.; Zacharias, M. J. Comput. Chem. 2009, 30, 479-492
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 479-492
-
-
Frickenhaus, S.1
Kannan, S.2
Zacharias, M.3
-
29
-
-
0033557181
-
-
Daura, X.; van Gunsteren, W. F.; Mark, A. E. Proteins 1999, 34, 269-280
-
(1999)
Proteins
, vol.34
, pp. 269-280
-
-
Daura, X.1
Van Gunsteren, W.F.2
Mark, A.E.3
-
30
-
-
67650299730
-
-
Batzoglou, S., Ed.; Springer: Berlin Lecture Notes in Computer Science, pp
-
Ramanathan, A.; Agarwal, P.; Kurnikova, M.; Langmead, C. In Research in Computational Molecular Biology; Batzoglou, S., Ed.; Springer: Berlin, 2009; Vol. 5541; Lecture Notes in Computer Science, pp 138-154.
-
(2009)
Research in Computational Molecular Biology
, vol.5541
, pp. 138-154
-
-
Ramanathan, A.1
Agarwal, P.2
Kurnikova, M.3
Langmead, C.4
-
31
-
-
77950854473
-
-
Ramanathan, A.; Agarwal, P. K.; Kurnikova, M.; Langmead, C. J. J. Comput. Biol. 2010, 17, 309-324
-
(2010)
J. Comput. Biol.
, vol.17
, pp. 309-324
-
-
Ramanathan, A.1
Agarwal, P.K.2
Kurnikova, M.3
Langmead, C.J.4
-
32
-
-
33749583360
-
-
Eliassi-Rad, T.; Ungar, L.; Craven, M.; Gunopulos, D., Eds. KDD '06; ACM: New York
-
Sun, J.; Tao, D.; Faloutsos, C. In Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining; Eliassi-Rad, T.; Ungar, L.; Craven, M.; Gunopulos, D., Eds.; KDD '06; ACM: New York, 2006; pp 374-383.
-
(2006)
Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
, pp. 374-383
-
-
Sun, J.1
Tao, D.2
Faloutsos, C.3
-
34
-
-
0029912748
-
-
Jorgensen, W.; Maxwell, D.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.1
Maxwell, D.2
Tirado-Rives, J.3
-
35
-
-
0000457975
-
-
Berweger, C. D.; van Gunsteren, W. F.; Müller-Plathe, F. Chem. Phys. Lett. 1995, 232, 429-436
-
(1995)
Chem. Phys. Lett.
, vol.232
, pp. 429-436
-
-
Berweger, C.D.1
Van Gunsteren, W.F.2
Müller-Plathe, F.3
-
36
-
-
40749131831
-
-
IEEE Computer Society: Los Alamitos, CA
-
Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. SC 2006 Conference, Proceedings of the ACM/IEEE; IEEE Computer Society: Los Alamitos, CA, 2006; p 43.
-
(2006)
SC 2006 Conference, Proceedings of the ACM/IEEE
, pp. 43
-
-
Bowers, K.J.1
Chow, E.2
Xu, H.3
Dror, R.O.4
Eastwood, M.P.5
Gregersen, B.A.6
Klepeis, J.L.7
Kolossvary, I.8
Moraes, M.A.9
Sacerdoti, F.D.10
Salmon, J.K.11
Shan, Y.12
Shaw, D.E.13
-
37
-
-
0035871686
-
-
Krautler, V.; van Gunsteren, W. F.; Hünenberger, P. J. Comput. Chem. 2001, 22, 501-508
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 501-508
-
-
Krautler, V.1
Van Gunsteren, W.F.2
Hünenberger, P.3
-
38
-
-
22944460220
-
-
Shan, Y.; Klepeis, J. L.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. J. Chem. Phys. 2005, 122, 054101
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 054101
-
-
Shan, Y.1
Klepeis, J.L.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
39
-
-
33745631543
-
-
Böhm, K.; Jensen, C. S.; Haas, L. M.; Kersten, M. L.; Larson, P.-å.; Ooi, B. C., Eds.; ACM: New York
-
Papadimitriou, S.; Sun, J.; Faloutsos, C. In Proceedings of the 31st International Conference on Very Large Data Bases, Trondheim, Norway; Böhm, K.; Jensen, C. S.; Haas, L. M.; Kersten, M. L.; Larson, P.-å.; Ooi, B. C., Eds.; ACM: New York, 2005; Vol. 31, pp 697-708.
-
(2005)
Proceedings of the 31st International Conference on Very Large Data Bases, Trondheim, Norway
, vol.31
, pp. 697-708
-
-
Papadimitriou, S.1
Sun, J.2
Faloutsos, C.3
-
40
-
-
19344375707
-
-
J. Wiley and Sons, Ltd.: West Sussex, England.
-
Smilde, A.; Bro, R.; Geladi, P. Multi-way Analysis: Applications in the Chemical Sciences; J. Wiley and Sons, Ltd.: West Sussex, England, 2004.
-
(2004)
Multi-way Analysis: Applications in the Chemical Sciences
-
-
Smilde, A.1
Bro, R.2
Geladi, P.3
-
42
-
-
0034500645
-
-
Hess, B. Phys. Rev. E 2000, 62, 8438-8448
-
(2000)
Phys. Rev. e
, vol.62
, pp. 8438-8448
-
-
Hess, B.1
-
44
-
-
45849131354
-
-
Lange, O. F.; Lakomek, N.-A.; Fares, C.; Schroder, G. F.; Walter, K. F. A.; Becker, S.; Meiler, J.; Grubmuller, H.; Griesinger, C.; de Groot, B. L. Science 2008, 320, 1471-1475
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.-A.2
Fares, C.3
Schroder, G.F.4
Walter, K.F.A.5
Becker, S.6
Meiler, J.7
Grubmuller, H.8
Griesinger, C.9
De Groot, B.L.10
-
47
-
-
73949097915
-
-
Wriggers, W.; Stafford, K. A.; Shan, Y.; Piana, S.; Maragakis, P.; Lindorff-Larsen, K.; Miller, P. J.; Gullingsrud, J.; Rendleman, C. A.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. J. Chem. Theory Comput. 2009, 5, 2595-2605
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2595-2605
-
-
Wriggers, W.1
Stafford, K.A.2
Shan, Y.3
Piana, S.4
Maragakis, P.5
Lindorff-Larsen, K.6
Miller, P.J.7
Gullingsrud, J.8
Rendleman, C.A.9
Eastwood, M.P.10
Dror, R.O.11
Shaw, D.E.12
-
48
-
-
79955752235
-
-
Technical Report CMU-CS-08-10, Carnegie Mellon University: Pittsburgh, PA.
-
Ramanathan, A.; Agarwal, P. K.; Langmead, C. J. Using tensor analysis to characterize contact-map dynamics in proteins; Technical Report CMU-CS-08-10, Carnegie Mellon University: Pittsburgh, PA, 2008.
-
(2008)
Using Tensor Analysis to Characterize Contact-map Dynamics in Proteins
-
-
Ramanathan, A.1
Agarwal, P.K.2
Langmead, C.J.3
-
51
-
-
79952582736
-
-
Gama, J.; Gaber, M. M., Eds.; Springer: New York,; Chapter 11, pp
-
Sun, J.; Papadimitriou, S.; Yu, P. S. In Learning from Data Streams: Processing Techniques in Sensor Networks; Gama, J.; Gaber, M. M., Eds.; Springer: New York, 2007; Chapter 11, pp 165-184.
-
(2007)
Learning from Data Streams: Processing Techniques in Sensor Networks
, pp. 165-184
-
-
Sun, J.1
Papadimitriou, S.2
Yu, P.S.3
-
52
-
-
43649093747
-
-
Yogurtcu, O. N.; Erdemli, S. B.; Nussinov, R.; Turkay, M.; Keskin, O. Biophys. J. 2008, 94, 3475-3485
-
(2008)
Biophys. J.
, vol.94
, pp. 3475-3485
-
-
Yogurtcu, O.N.1
Erdemli, S.B.2
Nussinov, R.3
Turkay, M.4
Keskin, O.5
-
53
-
-
58149218369
-
-
Narzi, D.; Daidone, I.; Amadei, A.; Di Nola, A. J. Chem. Theory Comput. 2008, 4, 1940-1948
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1940-1948
-
-
Narzi, D.1
Daidone, I.2
Amadei, A.3
Di Nola, A.4
-
54
-
-
77951680969
-
-
van der Kamp, M. W.; Schaeffer, R. D.; Jonsson, A. L.; Scouras, A. D.; Simms, A. M.; Toofanny, R. D.; Benson, N. C.; Anderson, P. C.; Merkley, E. D.; Rysavy, S.; Bromley, D.; Beck, D. A.; Daggett, V. Structure 2010, 18, 423-435
-
(2010)
Structure
, vol.18
, pp. 423-435
-
-
Van Der Kamp, M.W.1
Schaeffer, R.D.2
Jonsson, A.L.3
Scouras, A.D.4
Simms, A.M.5
Toofanny, R.D.6
Benson, N.C.7
Anderson, P.C.8
Merkley, E.D.9
Rysavy, S.10
Bromley, D.11
Beck, D.A.12
Daggett, V.13
-
55
-
-
0026320866
-
-
Frauenfelder, H.; Sligar, S.; Wolynes, P. Science 1991, 254, 1598-1603
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.2
Wolynes, P.3
-
57
-
-
0013153953
-
-
Technical Report CS-R9526; Centrum voor Wiskunde en Informatica (CWI): Amsterdam.
-
van Rossum, G. Python Reference Manual; Technical Report CS-R9526; Centrum voor Wiskunde en Informatica (CWI): Amsterdam, 1995.
-
(1995)
Python Reference Manual
-
-
Van Rossum, G.1
-
58
-
-
84875379930
-
-
R2009a; Mathworks: Natick, MA.
-
MATLAB, R2009a; Mathworks: Natick, MA, 2009.
-
(2009)
MATLAB
-
-
-
61
-
-
70350786551
-
A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories
-
SC' 08; IEEE: Piscataway, NJ
-
Tu, T.; Rendleman, C. A.; Borhani, D. W.; Dror, R. O.; Gullingsrud, J.; Jensen, M. O.; Klepeis, J. L.; Maragakis, P.; Miller, P.; Stafford, K. A.; Shaw, D. E. A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories; In Proceedings of ACM/IEEE Conference on Supercomputing; SC' 08; IEEE: Piscataway, NJ, 2008; pp 56: 1-12.
-
(2008)
Proceedings of ACM/IEEE Conference on Supercomputing
, pp. 1-56
-
-
Tu, T.1
Rendleman, C.A.2
Borhani, D.W.3
Dror, R.O.4
Gullingsrud, J.5
Jensen, M.O.6
Klepeis, J.L.7
Maragakis, P.8
Miller, P.9
Stafford, K.A.10
Shaw, D.E.11
-
62
-
-
34147192127
-
-
Grünberg, R.; Nilges, M.; Leckner, J. Bioinformatics 2007, 23, 769-770
-
(2007)
Bioinformatics
, vol.23
, pp. 769-770
-
-
Grünberg, R.1
Nilges, M.2
Leckner, J.3
|