-
1
-
-
33644559358
-
Enzymes: an integrated view of structure, dynamics and function
-
Agarwal, P.K. (2006) Enzymes: an integrated view of structure, dynamics and function. Microb. Cell Fact., 5, e2.
-
(2006)
Microb. Cell Fact.
, vol.5
-
-
Agarwal, P.K.1
-
2
-
-
4544353149
-
Application of time series analysis on molecular dynamics simulations of proteins: a study of different conformational spaces by principal component analysis
-
Alakent, B. et al. (2004) Application of time series analysis on molecular dynamics simulations of proteins: a study of different conformational spaces by principal component analysis. J. Chem. Phys., 121, 4759.
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 4759
-
-
Alakent, B.1
-
3
-
-
26944461146
-
Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. mimicking protein dynamics in different time scales
-
Alakent, B. et al. (2005a) Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. mimicking protein dynamics in different time scales. J. Chem. Phys., 123, 144910.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 144910
-
-
Alakent, B.1
-
4
-
-
26944473403
-
Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. investigation of explicit solvent effects
-
Alakent, B. et al. (2005b) Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. investigation of explicit solvent effects. J. Chem. Phys., 123, 144911.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 144911
-
-
Alakent, B.1
-
5
-
-
33846660784
-
Mimicking protein dynamics by the integration of elastic network model with time series analysis
-
Alakent, B. et al. (2007) Mimicking protein dynamics by the integration of elastic network model with time series analysis. Int. J. High Perform. Comput. Appl., 21, 59-65.
-
(2007)
Int. J. High Perform. Comput. Appl.
, vol.21
, pp. 59-65
-
-
Alakent, B.1
-
6
-
-
34147177681
-
Using FPGA devices to accelerate biomolecular simulations
-
Alam, S.R. et al. (2007) Using FPGA devices to accelerate biomolecular simulations. Computer, 40, 66-73.
-
(2007)
Computer
, vol.40
, pp. 66-73
-
-
Alam, S.R.1
-
7
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A. et al. (1993) Essential dynamics of proteins. Proteins: Struct. Funct. Genet., 17, 412-425.
-
(1993)
Proteins: Struct. Funct. Genet.
, vol.17
, pp. 412-425
-
-
Amadei, A.1
-
9
-
-
0029123975
-
Following protein folding in real time using NMR spectroscopy
-
Balbach, J. et al. (1995) Following protein folding in real time using NMR spectroscopy. Nat. Struct. Mol. Biol., 2, 865-870.
-
(1995)
Nat. Struct. Mol. Biol.
, vol.2
, pp. 865-870
-
-
Balbach, J.1
-
10
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsera, M. et al. (1996) Principal component analysis and long time protein dynamics. J. Phys. Chem., 100, 2567-2572.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2567-2572
-
-
Balsera, M.1
-
11
-
-
70449877805
-
Folding@home: lessons from eight years of volunteer distributed computing
-
Beberg, A.L. et al. (2009) Folding@home: lessons from eight years of volunteer distributed computing. IEEE Int. Symp. Parallel Distrib. Process., 1-8.
-
(2009)
IEEE Int. Symp. Parallel Distrib. Process.
, pp. 1-8
-
-
Beberg, A.L.1
-
12
-
-
0003608314
-
-
Springer-Verlag New York, Inc. Secaucus, NJ, USA
-
Blake, A. and Isard, M. (1998) Active Contours: The Application of Techniques from Graphics, Vision, and Control Theory and Statistics to Visual Tracking of Shapes in Motion. Springer-Verlag New York, Inc. Secaucus, NJ, USA.
-
(1998)
Active Contours: The Application of Techniques from Graphics, Vision, and Control Theory and Statistics to Visual Tracking of Shapes in Motion
-
-
Blake, A.1
Isard, M.2
-
13
-
-
77954635393
-
Protein folded states are kinetic hubs
-
Bowman, G.G.R. and Pande, V.S. (2010) Protein folded states are kinetic hubs. Proc. Natl Acad. Sci. USA, 107, 10890-10895.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 10890-10895
-
-
Bowman, G.G.R.1
Pande, V.S.2
-
14
-
-
17044443084
-
Accelerating molecular dynamics simulations by linear prediction of time series
-
Brutovsky, B. et al. (2003) Accelerating molecular dynamics simulations by linear prediction of time series. J. Chem. Phys., 118, 6179-6187.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 6179-6187
-
-
Brutovsky, B.1
-
15
-
-
0032612381
-
High-order contrasts for independent component analysis
-
Cardoso, J.-F. (1999) High-order contrasts for independent component analysis. Neural Comput., 11, 157-192.
-
(1999)
Neural Comput.
, vol.11
, pp. 157-192
-
-
Cardoso, J.-F.1
-
16
-
-
33749055796
-
Markov propagation of allosteric effects in biomolecular systems
-
Chennubhotla, C.S. and Bahar, I. (2006) Markov propagation of allosteric effects in biomolecular systems. Mol. Sys. Biol., 2, 36.
-
(2006)
Mol. Sys. Biol.
, vol.2
, pp. 36
-
-
Chennubhotla, C.S.1
Bahar, I.2
-
17
-
-
34547683322
-
Markov methods for hierarchical coarse graining of large protein dynamics
-
Chennubhotla, C.S. and Bahar, I. (2007a) Markov methods for hierarchical coarse graining of large protein dynamics. J. Comp. Biol., 14, 765-766.
-
(2007)
J. Comp. Biol.
, vol.14
, pp. 765-766
-
-
Chennubhotla, C.S.1
Bahar, I.2
-
18
-
-
34848882812
-
Signal propagation in proteins and relation to equilibrium fluctuations
-
Chennubhotla, C.S. and Bahar, I. (2007b) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput. Biol., 3, 1716-1726.
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 1716-1726
-
-
Chennubhotla, C.S.1
Bahar, I.2
-
19
-
-
84899011627
-
Eigencuts: half-lives of eigenflows for spectral clustering
-
Becker, S. et al. (eds), MIT Press, Cambridge, MA
-
Chennubhotla, C.S. and Jepson, A. (2003) Eigencuts: half-lives of eigenflows for spectral clustering. In Becker, S. et al. (eds) Advances in Neural Information Processing Systems (NIPS). MIT Press, Cambridge, MA, pp. 689-696.
-
(2003)
Advances in Neural Information Processing Systems (NIPS)
, pp. 689-696
-
-
Chennubhotla, C.S.1
Jepson, A.2
-
20
-
-
84898993973
-
Hierarchical eigensolver for transition matrices in spectral methods
-
Lawrence, K.S. et al. (eds), MIT Press, Cambridge, MA
-
Chennubhotla, C.S. and Jepson, A. (2005) Hierarchical eigensolver for transition matrices in spectral methods. In Lawrence, K.S. et al. (eds) Advances in Neural Information Processing Systems (NIPS). MIT Press, Cambridge, MA, pp. 273-280.
-
(2005)
Advances in Neural Information Processing Systems (NIPS)
, pp. 273-280
-
-
Chennubhotla, C.S.1
Jepson, A.2
-
21
-
-
77954202318
-
Markov dynamic models for long-timescale protein motion
-
Chiang, T.-H. et al. (2010) Markov dynamic models for long-timescale protein motion. Bioinformatics, 26, i269-i277.
-
(2010)
Bioinformatics
, vol.26
-
-
Chiang, T.-H.1
-
22
-
-
34247338100
-
Automatic discovery of metastable states for the construction of markov models of macromolecular conformational dynamics
-
Chodera, J.D. et al. (2007) Automatic discovery of metastable states for the construction of markov models of macromolecular conformational dynamics. J. Chem. Phys., 126, 155101.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
-
23
-
-
0023140044
-
Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin
-
Elber, R. and Karplus, M. (1987) Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science, 235, 318-321.
-
(1987)
Science
, vol.235
, pp. 318-321
-
-
Elber, R.1
Karplus, M.2
-
25
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder, H. et al. (1991) The energy landscapes and motions of proteins. Science, 254, 1598-1603.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
-
26
-
-
0004236492
-
-
Johns Hopkins University Press, Baltimore, MD, USA
-
Golub, G.H. and Van Loan, C.F. (1996) Matrix Computations. Johns Hopkins University Press, Baltimore, MD, USA.
-
(1996)
Matrix Computations
-
-
Golub, G.H.1
Van Loan, C.F.2
-
27
-
-
67650099787
-
Acemd: accelerating biomolecular dynamics in the microsecond time scale
-
Harvey, M.J. et al. (2009) Acemd: accelerating biomolecular dynamics in the microsecond time scale. J. Chem. Theory Comput., 5, 1632-1639.
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1632-1639
-
-
Harvey, M.J.1
-
28
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman, K. and Kern, D. (2007) Dynamic personalities of proteins. Nature, 450, 964-972.
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
29
-
-
79959383924
-
-
Master's thesis, University of Toronto, Toronto, Canada
-
Hyndman, M. (2007) Dynamic Texture Modelling. Master's thesis, University of Toronto, Toronto, Canada.
-
(2007)
Dynamic Texture Modelling
-
-
Hyndman, M.1
-
30
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M. and McCammon, J.A. (2002) Molecular dynamics simulations of biomolecules. Nat. Struct. Biol., 9, 646-652.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
31
-
-
22344432186
-
Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models
-
Kneller, G.R. (2005) Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models. Phys. Chem. Chem. Phys., 7, 2641-2655.
-
(2005)
Phys. Chem. Chem. Phys.
, vol.7
, pp. 2641-2655
-
-
Kneller, G.R.1
-
32
-
-
0035936357
-
Computing memory functions from molecular dynamics simulations
-
Kneller, G.R. and Hinsen, K. (2001) Computing memory functions from molecular dynamics simulations. J. Chem. Phys., 115, 11097-11105.
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 11097-11105
-
-
Kneller, G.R.1
Hinsen, K.2
-
33
-
-
33751219531
-
Can principal components yield a dimension reduced description of protein dynamics on long time scales?
-
Lange, O.F. and Grubmuller, H. (2006) Can principal components yield a dimension reduced description of protein dynamics on long time scales? J. Phys. Chem. B., 110, 22842-22852.
-
(2006)
J. Phys. Chem. B.
, vol.110
, pp. 22842-22852
-
-
Lange, O.F.1
Grubmuller, H.2
-
34
-
-
39749132831
-
Full correlation analysis of conformational protein dynamics
-
Lange, O. and Grubmuller, H. (2008) Full correlation analysis of conformational protein dynamics. Proteins, 70, 1294-1312.
-
(2008)
Proteins
, vol.70
, pp. 1294-1312
-
-
Lange, O.1
Grubmuller, H.2
-
35
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange, O.F. et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science, 320, 1471-1475.
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
-
36
-
-
0020200488
-
Molecular dynamics of ferrocytochrome c: anharmonicity of atomic displacements
-
Mao, B. et al. (1982) Molecular dynamics of ferrocytochrome c: anharmonicity of atomic displacements. Biopolymers, 21, 1979-1989.
-
(1982)
Biopolymers
, vol.21
, pp. 1979-1989
-
-
Mao, B.1
-
38
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J.C. et al. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem., 26, 1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
-
39
-
-
73349133343
-
Computational identification of slow conformational fluctuations in proteins
-
Ramanathan, A. and Agarwal, P.K. (2009) Computational identification of slow conformational fluctuations in proteins. J. Phys. Chem. B, 113, 16669-16680.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 16669-16680
-
-
Ramanathan, A.1
Agarwal, P.K.2
-
40
-
-
67650299730
-
An online approach for mining collective behaviors from molecular dynamics simulations
-
Springer, Berlin, Heidelberg
-
Ramanathan, A. et al. (2009) An online approach for mining collective behaviors from molecular dynamics simulations. In Research in Computational Molecular Biology (RECOMB), Vol. 5541 of Lecture Notes in Computer Science, Springer, Berlin, Heidelberg, pp. 138-154.
-
(2009)
Research in Computational Molecular Biology (RECOMB) of Lecture Notes in Computer Science
, vol.5541
, pp. 138-154
-
-
Ramanathan, A.1
-
41
-
-
79551506505
-
Discovering conformational sub-states relevant to protein function
-
Ramanathan, A. et al. (2011a) Discovering conformational sub-states relevant to protein function. PLoS ONE. 6, e15827.
-
(2011)
PLoS ONE
, vol.6
-
-
Ramanathan, A.1
-
42
-
-
79952594334
-
On-the-fly identification of conformational sub-states from molecular dynamics simulations
-
Ramanathan, A. et al. (2011b) On-the-fly identification of conformational sub-states from molecular dynamics simulations. J. Chem. Theory Comput., 7, 778-789.
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 778-789
-
-
Ramanathan, A.1
-
43
-
-
35348886062
-
Anton, a special-purpose machine for molecular dynamics simulation
-
Shaw, D.E. et al. (2007) Anton, a special-purpose machine for molecular dynamics simulation. SIGARCH Comput. Archit. News, 35, 1-12.
-
(2007)
SIGARCH Comput. Archit. News
, vol.35
, pp. 1-12
-
-
Shaw, D.E.1
-
44
-
-
0036286654
-
Free energy simulations come of age: protein-ligand recognition
-
Simonson, T. et al. (2002) Free energy simulations come of age: protein-ligand recognition. Acc. Chem. Res., 35, 430-437.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 430-437
-
-
Simonson, T.1
-
45
-
-
0034906622
-
Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase
-
Tai, K. et al. (2008) Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys. J., 81, 715-724.
-
(2008)
Biophys. J.
, vol.81
, pp. 715-724
-
-
Tai, K.1
-
46
-
-
77951680969
-
Dynameomics: a comprehensive database of protein dynamics
-
van der Kamp, M.W. et al. (2010) Dynameomics: a comprehensive database of protein dynamics. Structure, 18, 423-435.
-
(2010)
Structure
, vol.18
, pp. 423-435
-
-
van der Kamp, M.W.1
-
47
-
-
34247210226
-
Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide
-
West, A.M.A. et al. (2007) Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide. J. Chem. Phys., 126, 145104.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 145104
-
-
West, A.M.A.1
|