-
1
-
-
42149175435
-
Transition networks for modeling the kinetics of conformational change in macromolecules
-
F. Noé and S. Fischer, "Transition networks for modeling the kinetics of conformational change in macromolecules," Curr. Opin. Struct. Biol. 18, 154-162 (2008). 10.1016/j.sbi.2008.01.008
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 154-162
-
-
Noé, F.1
Fischer, S.2
-
2
-
-
84900548447
-
Markov state models of biomolecular conformational dynamics
-
J. D. Chodera and F. Noé, "Markov state models of biomolecular conformational dynamics," Curr. Opin. Struct. Biol. 25, 135-144 (2014). 10.1016/j.sbi.2014.04.002
-
(2014)
Curr. Opin. Struct. Biol.
, vol.25
, pp. 135-144
-
-
Chodera, J.D.1
Noé, F.2
-
3
-
-
3142707288
-
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
-
N. Singhal, C. D. Snow, and V. S. Pande, "Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin," J. Chem. Phys. 121, 415-425 (2004). 10.1063/1.1738647
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 415-425
-
-
Singhal, N.1
Snow, C.D.2
Pande, V.S.3
-
4
-
-
2942560604
-
Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and a β-hairpin peptide
-
W. C. Swope, J. W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov, and R. Zhou, "Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and a β -hairpin peptide," J. Phys. Chem. B 108, 6582-6594 (2004). 10.1021/jp037422q
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6582-6594
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
Pitman, M.4
Eleftheriou, M.5
Fitch, B.G.6
Germain, R.S.7
Rayshubski, A.8
Ward, T.J.C.9
Zhestkov, Y.10
Zhou, R.11
-
5
-
-
34247339716
-
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
-
F. Noé, I. Horenko, C. Schütte, and J. C. Smith, "Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states," J. Chem. Phys. 126, 155102 (2007). 10.1063/1.2714539
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155102
-
-
Noé, F.1
Horenko, I.2
Schütte, C.3
Smith, J.C.4
-
6
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, and W. C. Swope, "Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics," J. Chem. Phys. 126, 155101 (2007). 10.1063/1.2714538
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
7
-
-
44949178407
-
Coarse master equations for peptide folding dynamics
-
N.-V. Buchete and G. Hummer, "Coarse master equations for peptide folding dynamics," J. Phys. Chem. B 112, 6057-6069 (2008). 10.1021/jp0761665
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057-6069
-
-
Buchete, N.-V.1
Hummer, G.2
-
8
-
-
79955395931
-
What is the time scale for α-helix nucleation?
-
D. De Sancho and R. B. Best, "What is the time scale for α -helix nucleation?," J. Am. Chem. Soc. 133, 6809-6816 (2011). 10.1021/ja200834s
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 6809-6816
-
-
De Sancho, D.1
Best, R.B.2
-
9
-
-
79953167530
-
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
-
F. Noé, S. Doose, I. Daidone, M. Löllmann, M. Sauer, J. Chodera, and J. Smith, "Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments," Proc. Natl. Acad. Sci. U. S. A. 108, 4822-4827 (2011). 10.1073/pnas.1004646108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 4822-4827
-
-
Noé, F.1
Doose, S.2
Daidone, I.3
Löllmann, M.4
Sauer, M.5
Chodera, J.6
Smith, J.7
-
10
-
-
84903743025
-
Molecular origins of internal friction effects on protein-folding rates
-
D. De Sancho, A. Sirur, and R. B. Best, "Molecular origins of internal friction effects on protein-folding rates," Nat. Commun. 5, 4307 (2014). 10.1038/ncomms5307
-
(2014)
Nat. Commun.
, vol.5
, pp. 4307
-
-
De Sancho, D.1
Sirur, A.2
Best, R.B.3
-
12
-
-
80755172456
-
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories
-
T. J. Lane, G. R. Bowman, K. Beauchamp, V. A. Voelz, and V. S. Pande, "Markov state model reveals folding and functional dynamics in ultra-long MD trajectories," J. Am. Chem. Soc. 133, 18413-18419 (2011). 10.1021/ja207470h
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 18413-18419
-
-
Lane, T.J.1
Bowman, G.R.2
Beauchamp, K.3
Voelz, V.A.4
Pande, V.S.5
-
13
-
-
76149136021
-
Molecular simulation of ab initio protein folding for a millisecond folder NTL9 (1-39)
-
V. Voelz, G. Bowman, K. Beauchamp, and V. Pande, "Molecular simulation of ab initio protein folding for a millisecond folder NTL9 (1-39)," J. Am. Chem. Soc. 132, 1526-1528 (2010). 10.1021/ja9090353
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 1526-1528
-
-
Voelz, V.1
Bowman, G.2
Beauchamp, K.3
Pande, V.4
-
14
-
-
77950789652
-
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment
-
V. Voelz, V. Singh, W. Wedemeyer, L. Lapidus, and V. Pande, "Unfolded-state dynamics and structure of protein L characterized by simulation and experiment," J. Am. Chem. Soc. 132, 4702-4709 (2010). 10.1021/ja908369h
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 4702-4709
-
-
Voelz, V.1
Singh, V.2
Wedemeyer, W.3
Lapidus, L.4
Pande, V.5
-
15
-
-
84864495493
-
Slow unfolded-state structuring in ACBP folding revealed by simulation and experiment
-
V. A. Voelz, M. Jager, S. Yao, Y. Chen, L. Zhu, S. A. Waldauer, G. R. Bowman, M. Friedrichs, O. Bakajin, L. J. Lapidus, S. Weiss, and V. S. Pande, "Slow unfolded-state structuring in ACBP folding revealed by simulation and experiment," J. Am. Chem. Soc. 134, 12565-12577 (2012). 10.1021/ja302528z
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 12565-12577
-
-
Voelz, V.A.1
Jager, M.2
Yao, S.3
Chen, Y.4
Zhu, L.5
Waldauer, S.A.6
Bowman, G.R.7
Friedrichs, M.8
Bakajin, O.9
Lapidus, L.J.10
Weiss, S.11
Pande, V.S.12
-
16
-
-
79961218875
-
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments
-
K. Beauchamp, D. Ensign, R. Das, and V. Pande, "Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments," Proc. Natl. Acad. Sci. U. S. A. 108, 12734 (2011). 10.1073/pnas.1010880108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 12734
-
-
Beauchamp, K.1
Ensign, D.2
Das, R.3
Pande, V.4
-
17
-
-
84868122477
-
Simple few-state models reveal hidden complexity in protein folding
-
K. A. Beauchamp, R. McGibbon, Y.-S. Lin, and V. S. Pande, "Simple few-state models reveal hidden complexity in protein folding," Proc. Natl. Acad. Sci. U. S. A. 109, 17807-17813 (2012). 10.1073/pnas.1201810109
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 17807-17813
-
-
Beauchamp, K.A.1
McGibbon, R.2
Lin, Y.-S.3
Pande, V.S.4
-
18
-
-
84866599221
-
Evaluation and optimization of discrete state models of protein folding
-
E. H. Kellogg, O. F. Lange, and D. Baker, "Evaluation and optimization of discrete state models of protein folding," J. Phys. Chem. B 116, 11405-11413 (2012). 10.1021/jp3044303
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 11405-11413
-
-
Kellogg, E.H.1
Lange, O.F.2
Baker, D.3
-
19
-
-
84866152231
-
Quantifying hub-like behaviour in protein-folding networks
-
A. Dickson and C. L. Brooks, "Quantifying hub-like behaviour in protein-folding networks," J. Chem. Theory Comput. 8, 3044-3052 (2012). 10.1021/ct300537s
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3044-3052
-
-
Dickson, A.1
Brooks, C.L.2
-
20
-
-
84887076903
-
Engineering folding dynamics from two-state to downhill: Application to λ-repressor
-
J. W. Carter, C. M. Baker, R. B. Best, and D. De Sancho, "Engineering folding dynamics from two-state to downhill: Application to λ -repressor," J. Phys. Chem. B 117, 13435-13443 (2013). 10.1021/jp405904g
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 13435-13443
-
-
Carter, J.W.1
Baker, C.M.2
Best, R.B.3
De Sancho, D.4
-
21
-
-
84863939894
-
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
-
G. R. Bowman and P. L. Geissler, "Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites," Proc. Natl. Acad. Sci. U. S. A. 109, 11681-11686 (2012). 10.1073/pnas.1209309109
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 11681-11686
-
-
Bowman, G.R.1
Geissler, P.L.2
-
22
-
-
84890917722
-
Cloud-based simulations on google exacycle reveal ligand modulation of GPCR activation pathways
-
K. J. Kohlhoff, D. Shukla, M. Lawrenz, G. R. Bowman, D. E. Konerding, D. Belov, R. B. Altman, and V. S. Pande, "Cloud-based simulations on google exacycle reveal ligand modulation of GPCR activation pathways," Nat. Chem. 6, 15-21 (2014). 10.1038/nchem.1821
-
(2014)
Nat. Chem.
, vol.6
, pp. 15-21
-
-
Kohlhoff, K.J.1
Shukla, D.2
Lawrenz, M.3
Bowman, G.R.4
Konerding, D.E.5
Belov, D.6
Altman, R.B.7
Pande, V.S.8
-
23
-
-
78650193843
-
Quantitative analysis of ligand migration from transition networks
-
S. Mishra and M. Meuwly, "Quantitative analysis of ligand migration from transition networks," Biophys. J. 99, 3969-3978 (2010). 10.1016/j.bpj.2010.09.068
-
(2010)
Biophys. J.
, vol.99
, pp. 3969-3978
-
-
Mishra, S.1
Meuwly, M.2
-
25
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
I. Buch, T. Giorgino, and G. De Fabritiis, "Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations," Proc. Natl. Acad. Sci. U. S. A. 108, 10184-10189 (2011). 10.1073/pnas.1103547108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
26
-
-
84927947518
-
Identification of mutational hot spots for substrate diffusion: Application to myoglobin
-
D. De Sancho, A. Kubas, P.-H. Wang, J. Blumberger, and R. B. Best, "Identification of mutational hot spots for substrate diffusion: Application to myoglobin," J. Chem. Theory Comput. 11, 1919-1927 (2015). 10.1021/ct5011455
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 1919-1927
-
-
De Sancho, D.1
Kubas, A.2
Wang, P.-H.3
Blumberger, J.4
Best, R.B.5
-
27
-
-
73949085678
-
Rapid equilibrium sampling initiated from nonequilibrium data
-
X. Huang, G. R. Bowman, S. Bacallado, and V. S. Pande, "Rapid equilibrium sampling initiated from nonequilibrium data," Proc. Natl. Acad. Sci. U. S. A. 106, 19765-19769 (2009). 10.1073/pnas.0909088106
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 19765-19769
-
-
Huang, X.1
Bowman, G.R.2
Bacallado, S.3
Pande, V.S.4
-
28
-
-
77955817276
-
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics
-
A. J. DePaul, E. J. Thompson, S. S. Patel, K. Haldeman, and E. J. Sorin, "Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics," Nucleic Acids Res. 38, 4856-4867 (2010). 10.1093/nar/gkq134
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 4856-4867
-
-
Depaul, A.J.1
Thompson, E.J.2
Patel, S.S.3
Haldeman, K.4
Sorin, E.J.5
-
29
-
-
84862180145
-
Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations
-
A. A. Chen and A. E. García, "Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations," Proc. Natl. Acad. Sci. U. S. A. 109, E1530-E1539 (2012). 10.1073/pnas.1119552109
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. E1530-E1539
-
-
Chen, A.A.1
García, A.E.2
-
30
-
-
80053352142
-
Crystal structure of nucleotide-free dynamin
-
K. Faelber, Y. Posor, S. Gao, M. Held, Y. Roske, D. Schulze, V. Haucke, F. Noé, and O. Daumke, "Crystal structure of nucleotide-free dynamin," Nature 477, 556-560 (2011). 10.1038/nature10369
-
(2011)
Nature
, vol.477
, pp. 556-560
-
-
Faelber, K.1
Posor, Y.2
Gao, S.3
Held, M.4
Roske, Y.5
Schulze, D.6
Haucke, V.7
Noé, F.8
Daumke, O.9
-
31
-
-
80053979296
-
Msmbuilder2: Modeling conformational dynamics on the picosecond to millisecond scale
-
K. A. Beauchamp, G. R. Bowman, T. J. Lane, L. Maibaum, I. S. Haque, and V. S. Pande, "Msmbuilder2: Modeling conformational dynamics on the picosecond to millisecond scale," J. Chem. Theory Comput. 7, 3412-3419 (2011). 10.1021/ct200463m
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3412-3419
-
-
Beauchamp, K.A.1
Bowman, G.R.2
Lane, T.J.3
Maibaum, L.4
Haque, I.S.5
Pande, V.S.6
-
32
-
-
84863672816
-
Emma: A software package for Markov model building and analysis
-
M. Senne, B. Trendelkamp-Schroer, A. S. Mey, C. Schütte, and F. Noé, "Emma: A software package for Markov model building and analysis," J. Chem. Theory Comput. 8, 2223-2238 (2012). 10.1021/ct300274u
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2223-2238
-
-
Senne, M.1
Trendelkamp-Schroer, B.2
Mey, A.S.3
Schütte, C.4
Noé, F.5
-
33
-
-
79959830883
-
Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins
-
M. B. Borgia, A. Borgia, R. B. Best, A. Steward, D. Nettels, B. Wunderlich, B. Schuler, and J. Clarke, "Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins," Nature 474, 662-665 (2011). 10.1038/nature10099
-
(2011)
Nature
, vol.474
, pp. 662-665
-
-
Borgia, M.B.1
Borgia, A.2
Best, R.B.3
Steward, A.4
Nettels, D.5
Wunderlich, B.6
Schuler, B.7
Clarke, J.8
-
34
-
-
84947229753
-
Transient misfolding dominates multidomain protein folding
-
A. Borgia, K. R. Kemplen, M. B. Borgia, A. Soranno, S. Shammas, B. Wunderlich, D. Nettels, R. B. Best, J. Clarke, and B. Schuler, "Transient misfolding dominates multidomain protein folding," Nat. Commun. 6, 8861 (2015). 10.1038/ncomms9861
-
(2015)
Nat. Commun.
, vol.6
, pp. 8861
-
-
Borgia, A.1
Kemplen, K.R.2
Borgia, M.B.3
Soranno, A.4
Shammas, S.5
Wunderlich, B.6
Nettels, D.7
Best, R.B.8
Clarke, J.9
Schuler, B.10
-
35
-
-
84886081379
-
Identification of slow molecular order parameters for Markov model construction
-
G. Pérez-Hernández, F. Paul, T. Giorgino, G. De Fabritiis, and F. Noé, "Identification of slow molecular order parameters for Markov model construction," J. Chem. Phys. 139, 015102 (2013). 10.1063/1.4811489
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 015102
-
-
Pérez-Hernández, G.1
Paul, F.2
Giorgino, T.3
De Fabritiis, G.4
Noé, F.5
-
36
-
-
79959761281
-
Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?
-
P. Cossio, A. Laio, and F. Pietrucci, "Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?," Phys. Chem. Chem. Phys. 13, 10421-10425 (2011). 10.1039/c0cp02675a
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 10421-10425
-
-
Cossio, P.1
Laio, A.2
Pietrucci, F.3
-
37
-
-
84867316765
-
Deep architectures for protein contact map prediction
-
P. Di Lena, K. Nagata, and P. Baldi, "Deep architectures for protein contact map prediction," Bioinformatics 28, 2449-2457 (2012). 10.1093/bioinformatics/bts475
-
(2012)
Bioinformatics
, vol.28
, pp. 2449-2457
-
-
Di Lena, P.1
Nagata, K.2
Baldi, P.3
-
38
-
-
84873105668
-
Frustration in the energy landscapes of multidomain protein misfolding
-
W. Zheng, N. P. Schafer, and P. G. Wolynes, "Frustration in the energy landscapes of multidomain protein misfolding," Proc. Natl. Acad. Sci. U. S. A. 110, 1680-1685 (2013). 10.1073/pnas.1222130110
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 1680-1685
-
-
Zheng, W.1
Schafer, N.P.2
Wolynes, P.G.3
-
39
-
-
84890847498
-
Free energy landscapes for initiation and branching of protein aggregation
-
W. Zheng, N. P. Schafer, and P. G. Wolynes, "Free energy landscapes for initiation and branching of protein aggregation," Proc. Natl. Acad. Sci. U. S. A. 110, 20515-20520 (2013). 10.1073/pnas.1320483110
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 20515-20520
-
-
Zheng, W.1
Schafer, N.P.2
Wolynes, P.G.3
-
40
-
-
84896350914
-
Effects of interactions with the chaperonin cavity on protein folding and misfolding
-
A. Sirur, M. Knott, and R. B. Best, "Effects of interactions with the chaperonin cavity on protein folding and misfolding," Phys. Chem. Chem. Phys. 16, 6358-6366 (2014). 10.1039/C3CP52872C
-
(2014)
Phys. Chem. Chem. Phys.
, vol.16
, pp. 6358-6366
-
-
Sirur, A.1
Knott, M.2
Best, R.B.3
-
41
-
-
0036785556
-
The origins of asymmetry in the folding transition states of protein L and protein G
-
J. Karanicolas and C. L. Brooks, "The origins of asymmetry in the folding transition states of protein L and protein G," Protein Sci. 11, 2351-2361 (2002). 10.1110/ps.0205402
-
(2002)
Protein Sci.
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks, C.L.2
-
42
-
-
84874861633
-
Effects of interactions with the GroEL cavity on protein folding rates
-
A. Sirur and R. B. Best, "Effects of interactions with the GroEL cavity on protein folding rates," Biophys. J. 104, 1098-1106 (2013). 10.1016/j.bpj.2013.01.034
-
(2013)
Biophys. J.
, vol.104
, pp. 1098-1106
-
-
Sirur, A.1
Best, R.B.2
-
43
-
-
37549009571
-
Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding
-
Y. C. Kim and G. Hummer, "Coarse-grained models for simulations of multiprotein complexes: Application to ubiquitin binding," J. Mol. Biol. 375, 1416-1433 (2008). 10.1016/j.jmb.2007.11.063
-
(2008)
J. Mol. Biol.
, vol.375
, pp. 1416-1433
-
-
Kim, Y.C.1
Hummer, G.2
-
44
-
-
46249092554
-
Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, "Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation," J. Chem. Theory Comput. 4, 435-447 (2008). 10.1021/ct700301q
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
45
-
-
79957488000
-
Markov models of molecular kinetics: Generation and validation
-
J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J. D. Chodera, C. Schütte, and F. Noé, "Markov models of molecular kinetics: Generation and validation," J. Chem. Phys. 134, 174105 (2011). 10.1063/1.3565032
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.4
Senne, M.5
Held, M.6
Chodera, J.D.7
Schütte, C.8
Noé, F.9
-
46
-
-
84893405732
-
Data clustering: A review
-
A. K. Jain, M. N. Murty, and P. J. Flynn, "Data clustering: A review," ACM Comput. Surv. 31, 264-323 (1999). 10.1145/331499.331504
-
(1999)
ACM Comput. Surv.
, vol.31
, pp. 264-323
-
-
Jain, A.K.1
Murty, M.N.2
Flynn, P.J.3
-
47
-
-
13544256263
-
Robust Perron cluster analysis in conformation dynamics
-
P. Deuflhard and M. Weber, "Robust Perron cluster analysis in conformation dynamics," Linear Algebra Appl. 398, 161-184 (2005). 10.1016/j.laa.2004.10.026
-
(2005)
Linear Algebra Appl.
, vol.398
, pp. 161-184
-
-
Deuflhard, P.1
Weber, M.2
-
48
-
-
84859611714
-
Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements
-
K. Beauchamp, Y.-S. Lin, R. Das, and V. Pande, "Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements," J. Chem. Theory Comput. 8, 1409-1414 (2012). 10.1021/ct2007814
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1409-1414
-
-
Beauchamp, K.1
Lin, Y.-S.2
Das, R.3
Pande, V.4
-
49
-
-
84966454679
-
Depth-first search and linear graph algorithms
-
R. Tarjan, "Depth-first search and linear graph algorithms," SIAM J. Comput. 1, 146-160 (1972). 10.1137/0201010
-
(1972)
SIAM J. Comput.
, vol.1
, pp. 146-160
-
-
Tarjan, R.1
-
50
-
-
0034370539
-
Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains
-
P. Deuflhard, W. Huisinga, A. Fischer, and C. Schütte, "Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains," Linear Algebra Appl. 315, 39-59 (2000). 10.1016/S0024-3795(00)00095-1
-
(2000)
Linear Algebra Appl.
, vol.315
, pp. 39-59
-
-
Deuflhard, P.1
Huisinga, W.2
Fischer, A.3
Schütte, C.4
-
53
-
-
84969361029
-
-
See supplementary material at http://dx.doi.org/10.1063/1.4941579 E-JCPSA6-144-015607 for three supporting figures showing the robustness of the model with respect to lag time and amount of data used, and the relaxation times for the strongly connected component for each confinement scenario.
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