-
1
-
-
0034623787
-
Screen Savers of the World Unite!
-
Shirts, M.; Pande, V. S. Screen Savers of the World Unite! Science 2000, 290, 1903-1904 10.1126/science.290.5498.1903
-
(2000)
Science
, vol.290
, pp. 1903-1904
-
-
Shirts, M.1
Pande, V.S.2
-
2
-
-
77949978021
-
High-throughput all-atom molecular dynamics simulations using distributed computing
-
Buch, I.; Harvey, M. J.; Giorgino, T.; Anderson, D. P.; De Fabritiis, G. High-throughput all-atom molecular dynamics simulations using distributed computing J. Chem. Inf. Model. 2010, 50, 397-403 10.1021/ci900455r
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 397-403
-
-
Buch, I.1
Harvey, M.J.2
Giorgino, T.3
Anderson, D.P.4
De Fabritiis, G.5
-
3
-
-
77957937199
-
Atomic-Level Characterization of the Structural Dynamics of Proteins
-
Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R.; Eastwood, M.; Bank, J.; Jumper, J.; Salmon, J.; Shan, Y.; Wriggers, W. Atomic-Level Characterization of the Structural Dynamics of Proteins Science 2010, 330, 341-346 10.1126/science.1187409
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.5
Eastwood, M.6
Bank, J.7
Jumper, J.8
Salmon, J.9
Shan, Y.10
Wriggers, W.11
-
4
-
-
83155173599
-
-
Proceedings of the 2011 ACM/IEEE conference on Supercomputing. Seattle, WA.
-
Mei, C.; Sun, Y.; Zheng, G.; Bohm, E. J.; Laxmikant, K.; Phillips, J. C.; Harrison, C. Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime. Proceedings of the 2011 ACM/IEEE conference on Supercomputing. Seattle, WA, 2011.
-
(2011)
Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with A Multicore-optimized Message-driven Runtime
-
-
Mei, C.1
Sun, Y.2
Zheng, G.3
Bohm, E.J.4
Laxmikant, K.5
Phillips, J.C.6
Harrison, C.7
-
5
-
-
84868214675
-
SPFP: Speed without compromise - A mixed precision model for GPU accelerated molecular dynamics simulations
-
Le Grand, S.; Goetz, A. W.; Walker, R. C. SPFP: Speed without compromise-a mixed precision model for GPU accelerated molecular dynamics simulations Comput. Phys. Commun. 2013, 184, 374-380 10.1016/j.cpc.2012.09.022
-
(2013)
Comput. Phys. Commun.
, vol.184
, pp. 374-380
-
-
Le Grand, S.1
Goetz, A.W.2
Walker, R.C.3
-
6
-
-
84900552634
-
On-The-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations
-
Doerr, S.; De Fabritiis, G. On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations J. Chem. Theory Comput. 2014, 10, 2064-2069 10.1021/ct400919u
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 2064-2069
-
-
Doerr, S.1
De Fabritiis, G.2
-
7
-
-
84906569206
-
Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics
-
Preto, J.; Clementi, C. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics Phys. Chem. Chem. Phys. 2014, 16, 19181-19191 10.1039/C3CP54520B
-
(2014)
Phys. Chem. Chem. Phys.
, vol.16
, pp. 19181-19191
-
-
Preto, J.1
Clementi, C.2
-
8
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 2013, 29, 845-854 10.1093/bioinformatics/btt055
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Páll, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
Hess, B.11
Lindahl, E.12
-
9
-
-
84986563426
-
Protein conformational plasticity and complex ligand binding kinetics explored by atomistic simulations and Markov models
-
Plattner, N.; Noé, F. Protein conformational plasticity and complex ligand binding kinetics explored by atomistic simulations and Markov models Nat. Commun. 2015, 6, 7653 10.1038/ncomms8653
-
(2015)
Nat. Commun.
, vol.6
, pp. 7653
-
-
Plattner, N.1
Noé, F.2
-
10
-
-
84931287882
-
Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform
-
Pronk, S.; Pouya, I.; Lundborg, M.; Rotskoff, G.; Wesén, B.; Kasson, P. M.; Lindahl, E. Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform J. Chem. Theory Comput. 2015, 11, 2600-2608 10.1021/acs.jctc.5b00234
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 2600-2608
-
-
Pronk, S.1
Pouya, I.2
Lundborg, M.3
Rotskoff, G.4
Wesén, B.5
Kasson, P.M.6
Lindahl, E.7
-
11
-
-
84964649164
-
HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
-
Doerr, S.; Harvey, M. J.; Noé, F.; De Fabritiis, G. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery J. Chem. Theory Comput. 2016, 12, 1845-1852 10.1021/acs.jctc.6b00049
-
(2016)
J. Chem. Theory Comput.
, vol.12
, pp. 1845-1852
-
-
Doerr, S.1
Harvey, M.J.2
Noé, F.3
De Fabritiis, G.4
-
12
-
-
84949657891
-
FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs
-
Zimmerman, M. I.; Bowman, G. R. FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs J. Chem. Theory Comput. 2015, 11, 5747-5757 10.1021/acs.jctc.5b00737
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 5747-5757
-
-
Zimmerman, M.I.1
Bowman, G.R.2
-
13
-
-
70450255797
-
Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations
-
Noé, F.; Schütte, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 19011-19016 10.1073/pnas.0905466106
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 19011-19016
-
-
Noé, F.1
Schütte, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
14
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch, I.; Giorgino, T.; De Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 10184-10189 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
-
15
-
-
84863939894
-
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
-
Bowman, G. R.; Geissler, P. L. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 11681-11686 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
-
16
-
-
84928697282
-
Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
-
Gu, S.; Silva, D.-A.; Meng, L.; Yue, A.; Huang, X. Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis PLoS Comput. Biol. 2014, 10, e1003767 10.1371/journal.pcbi.1003767
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003767
-
-
Gu, S.1
Silva, D.-A.2
Meng, L.3
Yue, A.4
Huang, X.5
-
17
-
-
0000573002
-
A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo
-
Schütte, C.; Fischer, A.; Huisinga, W.; Deuflhard, P. A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo J. Comput. Phys. 1999, 151, 146-168 10.1006/jcph.1999.6231
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 146-168
-
-
Schütte, C.1
Fischer, A.2
Huisinga, W.3
Deuflhard, P.4
-
18
-
-
13544256263
-
-
In; Dellnitz, M. Kirkland, S. Neumann, M. Schütte, C. Elsevier: New York, Vol.
-
Deuflhard, P.; Weber, M. In Linear Algebra Applications; Dellnitz, M.; Kirkland, S.; Neumann, M.; Schütte, C., Eds.; Elsevier: New York, 2005; Vol. 398C; pp 161-184.
-
(2005)
Linear Algebra Applications
, vol.398
, pp. 161-184
-
-
Deuflhard, P.1
Weber, M.2
-
19
-
-
33746899725
-
Obtaining reaction coordinates by likelihood maximization
-
Peters, B.; Trout, B. L. Obtaining reaction coordinates by likelihood maximization J. Chem. Phys. 2006, 125, 054108 10.1063/1.2234477
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 054108
-
-
Peters, B.1
Trout, B.L.2
-
20
-
-
33745611125
-
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
-
Das, P.; Moll, M.; Stamati, H.; Kavraki, L. E.; Clementi, C. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 9885-9890 10.1073/pnas.0603553103
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, pp. 9885-9890
-
-
Das, P.1
Moll, M.2
Stamati, H.3
Kavraki, L.E.4
Clementi, C.5
-
21
-
-
34247339716
-
Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States
-
Noé, F.; Horenko, I.; Schütte, C.; Smith, J. C. Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States J. Chem. Phys. 2007, 126, 155102 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
-
22
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
Chodera, J. D.; Dill, K. A.; Singhal, N.; Pande, V. S.; Swope, W. C.; Pitera, J. W. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics J. Chem. Phys. 2007, 126, 155101 10.1063/1.2714538
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
Dill, K.A.2
Singhal, N.3
Pande, V.S.4
Swope, W.C.5
Pitera, J.W.6
-
23
-
-
44949178407
-
Coarse Master Equations for Peptide Folding Dynamics
-
Buchete, N. V.; Hummer, G. Coarse Master Equations for Peptide Folding Dynamics J. Phys. Chem. B 2008, 112, 6057-6069 10.1021/jp0761665
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057-6069
-
-
Buchete, N.V.1
Hummer, G.2
-
24
-
-
34547297406
-
Dihedral angle principal component analysis of molecular dynamics simulations
-
Altis, A.; Nguyen, P. H.; Hegger, R.; Stock, G. Dihedral angle principal component analysis of molecular dynamics simulations J. Chem. Phys. 2007, 126, 244111 10.1063/1.2746330
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 244111
-
-
Altis, A.1
Nguyen, P.H.2
Hegger, R.3
Stock, G.4
-
25
-
-
77449099723
-
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
-
Stamati, H.; Clementi, C.; Kavraki, L. E. Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides Proteins: Struct., Funct., Genet. 2010, 78, 223-235 10.1002/prot.22526
-
(2010)
Proteins: Struct., Funct., Genet.
, vol.78
, pp. 223-235
-
-
Stamati, H.1
Clementi, C.2
Kavraki, L.E.3
-
26
-
-
84903361996
-
Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules
-
Noé, F.; Wu, H.; Prinz, J.-H.; Plattner, N. Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules J. Chem. Phys. 2013, 139, 184114 10.1063/1.4828816
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 184114
-
-
Noé, F.1
Wu, H.2
Prinz, J.-H.3
Plattner, N.4
-
27
-
-
80053979296
-
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale
-
Beauchamp, K. A.; Bowman, G. R.; Lane, T. J.; Maibaum, L.; Haque, I. S.; Pande, V. S. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale J. Chem. Theory Comput. 2011, 7, 3412-3419 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
-
28
-
-
84863672816
-
EMMA - A software package for Markov model building and analysis
-
Senne, M.; Trendelkamp-Schroer, B.; Mey, A. S. J. S.; Schütte, C.; Noé, F. EMMA-A software package for Markov model building and analysis J. Chem. Theory Comput. 2012, 8, 2223-2238 10.1021/ct300274u
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2223-2238
-
-
Senne, M.1
Trendelkamp-Schroer, B.2
Mey, A.S.J.S.3
Schütte, C.4
Noé, F.5
-
29
-
-
84879735744
-
A variational approach to modeling slow processes in stochastic dynamical systems
-
Noé, F.; Nüske, F. A variational approach to modeling slow processes in stochastic dynamical systems Multiscale Model. Simul. 2013, 11, 635-655 10.1137/110858616
-
(2013)
Multiscale Model. Simul.
, vol.11
, pp. 635-655
-
-
Noé, F.1
Nüske, F.2
-
30
-
-
84875991078
-
Discovering mountain passes via torchlight: Methods for the definition of reaction coordinates and pathways in complex macromolecular reactions
-
Rohrdanz, M. A.; Zheng, W.; Clementi, C. Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions Annu. Rev. Phys. Chem. 2013, 64, 295-316 10.1146/annurev-physchem-040412-110006
-
(2013)
Annu. Rev. Phys. Chem.
, vol.64
, pp. 295-316
-
-
Rohrdanz, M.A.1
Zheng, W.2
Clementi, C.3
-
31
-
-
79953320021
-
Determination of reaction coordinates via locally scaled diffusion map
-
Rohrdanz, M. A.; Zheng, W.; Maggioni, M.; Clementi, C. Determination of reaction coordinates via locally scaled diffusion map J. Chem. Phys. 2011, 134, 124116 10.1063/1.3569857
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 124116
-
-
Rohrdanz, M.A.1
Zheng, W.2
Maggioni, M.3
Clementi, C.4
-
34
-
-
79958151345
-
Markov State Models Based on Milestoning
-
Schütte, C.; Noé, F.; Lu, J.; Sarich, M.; Vanden-Eijnden, E. Markov State Models Based on Milestoning J. Chem. Phys. 2011, 134, 204105 10.1063/1.3590108
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 204105
-
-
Schütte, C.1
Noé, F.2
Lu, J.3
Sarich, M.4
Vanden-Eijnden, E.5
-
35
-
-
84886081379
-
Identification of slow molecular order parameters for Markov model construction
-
Perez-Hernandez, G.; Paul, F.; Giorgino, T.; De Fabritiis, G.; Noé, F. Identification of slow molecular order parameters for Markov model construction J. Chem. Phys. 2013, 139, 015102 10.1063/1.4811489
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 015102
-
-
Perez-Hernandez, G.1
Paul, F.2
Giorgino, T.3
De Fabritiis, G.4
Noé, F.5
-
36
-
-
84876005630
-
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
-
Schwantes, C. R.; Pande, V. S. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9 J. Chem. Theory Comput. 2013, 9, 2000-2009 10.1021/ct300878a
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2000-2009
-
-
Schwantes, C.R.1
Pande, V.S.2
-
37
-
-
84946887423
-
PyEMMA 2: A software package for estimation, validation and analysis of Markov models
-
Scherer, M. K.; Trendelkamp-Schroer, B.; Paul, F.; Perez-Hernandez, G.; Hoffmann, M.; Plattner, N.; Prinz, J.-H.; Noé, F.; Wehmeyer, C. PyEMMA 2: A software package for estimation, validation and analysis of Markov models J. Chem. Theory Comput. 2015, 11, 5525-5542 10.1021/acs.jctc.5b00743
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 5525-5542
-
-
Scherer, M.K.1
Trendelkamp-Schroer, B.2
Paul, F.3
Perez-Hernandez, G.4
Hoffmann, M.5
Plattner, N.6
Prinz, J.-H.7
Noé, F.8
Wehmeyer, C.9
-
38
-
-
84944046499
-
Kinetic distance and kinetic maps from molecular dynamics simulation
-
Noé, F.; Clementi, C. Kinetic distance and kinetic maps from molecular dynamics simulation J. Chem. Theory Comput. 2015, 22, 5002-5011 10.1021/acs.jctc.5b00553
-
(2015)
J. Chem. Theory Comput.
, vol.22
, pp. 5002-5011
-
-
Noé, F.1
Clementi, C.2
-
39
-
-
84949638655
-
Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps
-
Boninsegna, L.; Gobbo, G.; Noé, F.; Clementi, C. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps J. Chem. Theory Comput. 2015, 11, 5947-5960 10.1021/acs.jctc.5b00749
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 5947-5960
-
-
Boninsegna, L.1
Gobbo, G.2
Noé, F.3
Clementi, C.4
-
40
-
-
79957488000
-
Markov models of molecular kinetics: Generation and Validation
-
Prinz, J.-H.; Wu, H.; Sarich, M.; Keller, B. G.; Senne, M.; Held, M.; Chodera, J. D.; Schütte, C.; Noé, F. Markov models of molecular kinetics: Generation and Validation J. Chem. Phys. 2011, 134, 174105 10.1063/1.3565032
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.G.4
Senne, M.5
Held, M.6
Chodera, J.D.7
Schütte, C.8
Noé, F.9
-
41
-
-
84922674715
-
Modeling Molecular Kinetics with tICA and the Kernel Trick
-
Schwantes, C. R.; Pande, V. S. Modeling Molecular Kinetics with tICA and the Kernel Trick J. Chem. Theory Comput. 2015, 11, 600-608 10.1021/ct5007357
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 600-608
-
-
Schwantes, C.R.1
Pande, V.S.2
-
42
-
-
0347243182
-
Nonlinear Component Analysis as a Kernel Eigenvalue Problem
-
Schölkopf, B.; Smola, A.; Müller, K.-R. Nonlinear Component Analysis as a Kernel Eigenvalue Problem Neural Comput. 1998, 10, 1299-1319 10.1162/089976698300017467
-
(1998)
Neural Comput.
, vol.10
, pp. 1299-1319
-
-
Schölkopf, B.1
Smola, A.2
Müller, K.-R.3
-
43
-
-
84898431921
-
Variational Approach to Molecular Kinetics
-
Nüske, F.; Keller, B. G.; Pérez-Hernández, G.; Mey, A. S. J. S.; Noé, F. Variational Approach to Molecular Kinetics J. Chem. Theory Comput. 2014, 10, 1739-1752 10.1021/ct4009156
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1739-1752
-
-
Nüske, F.1
Keller, B.G.2
Pérez-Hernández, G.3
Mey, A.S.J.S.4
Noé, F.5
-
44
-
-
84957072943
-
Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems
-
Nüske, F.; Schneider, R.; Vitalini, F.; Noé, F. Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems J. Chem. Phys. 2015, 144, 054105 10.1063/1.4940774
-
(2015)
J. Chem. Phys.
, vol.144
, pp. 054105
-
-
Nüske, F.1
Schneider, R.2
Vitalini, F.3
Noé, F.4
-
45
-
-
77956841151
-
On the approximation quality of Markov state models
-
Sarich, M.; Noé, F.; Schütte, C. On the approximation quality of Markov state models Multiscale Model. Simul. 2010, 8, 1154-1177 10.1137/090764049
-
(2010)
Multiscale Model. Simul.
, vol.8
, pp. 1154-1177
-
-
Sarich, M.1
Noé, F.2
Schütte, C.3
-
46
-
-
84921367680
-
Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models to Elucidate Conformational Dynamics of Multibody Systems
-
Sheong, F. K.; Silva, D.-A.; Meng, L.; Zhao, Y.; Huang, X. Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems J. Chem. Theory Comput. 2015, 11, 17-27 10.1021/ct5007168
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 17-27
-
-
Sheong, F.K.1
Silva, D.-A.2
Meng, L.3
Zhao, Y.4
Huang, X.5
-
47
-
-
84961290952
-
Variational cross-validation of slow dynamical modes in molecular kinetics
-
McGibbon, R. T.; Pande, V. S. Variational cross-validation of slow dynamical modes in molecular kinetics J. Chem. Phys. 2015, 142, 124105 10.1063/1.4916292
-
(2015)
J. Chem. Phys.
, vol.142
, pp. 124105
-
-
McGibbon, R.T.1
Pande, V.S.2
-
49
-
-
0000302959
-
Separation of a mixture of independent signals using time delayed correlations
-
Molgedey, L.; Schuster, H. G. Separation of a mixture of independent signals using time delayed correlations Phys. Rev. Lett. 1994, 72, 3634-3637 10.1103/PhysRevLett.72.3634
-
(1994)
Phys. Rev. Lett.
, vol.72
, pp. 3634-3637
-
-
Molgedey, L.1
Schuster, H.G.2
-
50
-
-
19644394100
-
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
-
Coifman, R. R.; Lafon, S.; Lee, A. B.; Maggioni, M.; Nadler, B.; Warner, F.; Zucker, S. W. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 7426-7431 10.1073/pnas.0500334102
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 7426-7431
-
-
Coifman, R.R.1
Lafon, S.2
Lee, A.B.3
Maggioni, M.4
Nadler, B.5
Warner, F.6
Zucker, S.W.7
-
51
-
-
84864071145
-
Diffusion Maps, Spectral Clustering and Eigenfunctions of Fokker-Planck Operators
-
Nadler, B.; Lafon, S.; Coifman, R. R.; Kevrekidis, I. G. Diffusion Maps, Spectral Clustering and Eigenfunctions of Fokker-Planck Operators Adv. Neural Inf. Process. Syst. (NIPS) 2005, 955-962
-
(2005)
Adv. Neural Inf. Process. Syst. (NIPS)
, pp. 955-962
-
-
Nadler, B.1
Lafon, S.2
Coifman, R.R.3
Kevrekidis, I.G.4
-
52
-
-
17444389688
-
Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations
-
Sriraman, S.; Kevrekidis, I. G.; Hummer, G. Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations J. Phys. Chem. B 2005, 109, 6479-6484 10.1021/jp046448u
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6479-6484
-
-
Sriraman, S.1
Kevrekidis, I.G.2
Hummer, G.3
-
53
-
-
84907992130
-
Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations
-
Suárez, D.; Díaz, N. Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations J. Chem. Theory Comput. 2014, 10, 4718-4729 10.1021/ct500700d
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 4718-4729
-
-
Suárez, D.1
Díaz, N.2
|