-
1
-
-
67650500988
-
The Biomolecular Simulation Program
-
Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. The Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-1614
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
MacKerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
2
-
-
0029011701
-
A 2nd Generation Force-Field for the Simulation of Protein, Nucleic-Acids, and Organic-Molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A 2nd Generation Force-Field for the Simulation of Protein, Nucleic-Acids, and Organic-Molecules J. Am. Chem. Soc. 1995, 117 (19) 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, Issue.19
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.J.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
3
-
-
34548283148
-
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
-
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. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. In SC 2006 Conference, Proceedings of the ACM/IEEE, IEEE, 2006, p 43.
-
(2006)
SC 2006 Conference, Proceedings of the ACM/IEEE, 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
-
4
-
-
80055081145
-
How Fast-Folding Proteins Fold
-
Lindorff-Larsen, K.; Piana, S.; Dror, R.; Shaw, D. E. How Fast-Folding Proteins Fold Science 2011, 334 (6055) 517-520
-
(2011)
Science
, vol.334
, Issue.6055
, pp. 517-520
-
-
Lindorff-Larsen, K.1
Piana, S.2
Dror, R.3
Shaw, D.E.4
-
5
-
-
0003166498
-
Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics
-
Chan, H. S.; Dill, K. A. Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics Proteins: Struct., Funct., Genet. 1998, 30 (1) 2-33
-
(1998)
Proteins: Struct., Funct., Genet.
, vol.30
, Issue.1
, pp. 2-33
-
-
Chan, H.S.1
Dill, K.A.2
-
6
-
-
0009586942
-
Understanding Protein Folding via Free-Energy Surfaces from Theory and Experiment
-
Dinner, A. R.; Sali, A.; Smith, L. J.; Dobson, C. M.; Karplus, M. Understanding Protein Folding via Free-Energy Surfaces from Theory and Experiment Trends Biochem. Sci. 2000, 25 (7) 331-339
-
(2000)
Trends Biochem. Sci.
, vol.25
, Issue.7
, pp. 331-339
-
-
Dinner, A.R.1
Sali, A.2
Smith, L.J.3
Dobson, C.M.4
Karplus, M.5
-
7
-
-
0030628825
-
Theory of Protein Folding: The Energy Landscape Perspective
-
Onuchic, J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Theory of Protein Folding: The Energy Landscape Perspective Annu. Rev. Phys. Chem. 1997, 48, 545-600
-
(1997)
Annu. Rev. Phys. Chem.
, vol.48
, pp. 545-600
-
-
Onuchic, J.N.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
8
-
-
0344301982
-
Protein Folding: A Perspective from Theory and Experiment
-
Dobson, C. M.; Sali, A.; Karplus, M. Protein Folding: A Perspective from Theory and Experiment Angew. Chem., Int. Ed. 1998, 37 (7) 868-893
-
(1998)
Angew. Chem., Int. Ed.
, vol.37
, Issue.7
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
9
-
-
0034743155
-
From Folding Theories to Folding Proteins: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding
-
Shea, J. E.; Brooks, I. C. L. From Folding Theories to Folding Proteins: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding Annu. Rev. Phys. Chem. 2001, 52 (7) 499-535
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, Issue.7
, pp. 499-535
-
-
Shea, J.E.1
Brooks, I.C.L.2
-
10
-
-
0000370391
-
The Topology of Multidimensional Potential Energy Surfaces: Theory and Application to Peptide Structure and Kinetics
-
Becker, O. M.; Karplus, M. The Topology of Multidimensional Potential Energy Surfaces: Theory and Application to Peptide Structure and Kinetics J. Chem. Phys. 1997, 106 (4) 1495-1517
-
(1997)
J. Chem. Phys.
, vol.106
, Issue.4
, pp. 1495-1517
-
-
Becker, O.M.1
Karplus, M.2
-
11
-
-
0037460544
-
Free Energy Landscapes of Model Peptides and Proteins
-
Evans, D.; Wales, D. J. Free Energy Landscapes of Model Peptides and Proteins J. Chem. Phys. 2003, 118 (8) 3891-3897
-
(2003)
J. Chem. Phys.
, vol.118
, Issue.8
, pp. 3891-3897
-
-
Evans, D.1
Wales, D.J.2
-
13
-
-
0037115811
-
Free Energy Disconnectivity Graphs: Application to Peptide Models
-
Krivov, S. V.; Karplus, M. Free Energy Disconnectivity Graphs: Application to Peptide Models J. Chem. Phys. 2002, 117 (23) 10894-10903
-
(2002)
J. Chem. Phys.
, vol.117
, Issue.23
, pp. 10894-10903
-
-
Krivov, S.V.1
Karplus, M.2
-
14
-
-
15744390440
-
Graphic Representation of Equilibrium and Kinetics in Oligopeptides: Time-Dependent Free Energy Disconnectivity Graphs
-
Kolchanov, N. Hofestaedt, R. Kluwer Academic Publishers: Boston
-
Gavrilov, A. V.; Chekmarev, S. F. Graphic Representation of Equilibrium and Kinetics in Oligopeptides: Time-Dependent Free Energy Disconnectivity Graphs. In Bioinformatics of Genome Regulation and Structure; Kolchanov, N.; Hofestaedt, R., Eds.; Kluwer Academic Publishers: Boston, 2002; pp 171-178.
-
(2002)
Bioinformatics of Genome Regulation and Structure
, pp. 171-178
-
-
Gavrilov, A.V.1
Chekmarev, S.F.2
-
15
-
-
6944235051
-
Hidden Complexity of Free Energy Surfaces for Peptide (Protein) Folding
-
Krivov, S. V.; Karplus, M. Hidden Complexity of Free Energy Surfaces for Peptide (Protein) Folding Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (41) 14766-14770
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, Issue.41
, pp. 14766-14770
-
-
Krivov, S.V.1
Karplus, M.2
-
16
-
-
34247338100
-
Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics
-
Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics Proc. Natl. Acad. Sci. U.S.A. 2007, 126 (15) 155101
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.126
, Issue.15
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
17
-
-
33746567202
-
One-Dimensional Free-Energy Profiles of Complex Systems: Progress Variables That Preserve the Barriers
-
Krivov, S. V.; Karplus, M. One-Dimensional Free-Energy Profiles of Complex Systems: Progress Variables That Preserve the Barriers J. Phys. Chem. B 2006, 110 (25) 12689-12698
-
(2006)
J. Phys. Chem. B
, vol.110
, Issue.25
, pp. 12689-12698
-
-
Krivov, S.V.1
Karplus, M.2
-
19
-
-
0034704229
-
A Global Geometric Framework for Nonlinear Dimensionality Reduction
-
Tenenbaum, J. B.; de Silva, V.; Langford, J. A Global Geometric Framework for Nonlinear Dimensionality Reduction Science 2000, 290 (5500) 2319-2323
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2319-2323
-
-
Tenenbaum, J.B.1
De Silva, V.2
Langford, J.3
-
20
-
-
84899009769
-
Global versus Local Methods in Nonlinear Dimensionality Reduction
-
De Silva, V.; Tenenbaum, J. B. Global versus Local Methods in Nonlinear Dimensionality Reduction Adv. Neural Inf. Process. Syst. 2003, 15, 705-712
-
(2003)
Adv. Neural Inf. Process. Syst.
, vol.15
, pp. 705-712
-
-
De Silva, V.1
Tenenbaum, J.B.2
-
21
-
-
0034704222
-
Nonlinear Dimensionality Reduction by Locally Linear Embedding
-
Roweis, S. T.; Saul, L. K. Nonlinear Dimensionality Reduction by Locally Linear Embedding Science 2000, 290 (5500) 2323-2326
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2323-2326
-
-
Roweis, S.T.1
Saul, L.K.2
-
22
-
-
0037948870
-
Hessian Eigenmaps: Locally Linear Embedding Techniques for High-Dimensional Data
-
Donoho, D. L.; Grimes, C. Hessian Eigenmaps: Locally Linear Embedding Techniques for High-Dimensional Data Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (10) 5591-5596
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, Issue.10
, pp. 5591-5596
-
-
Donoho, D.L.1
Grimes, C.2
-
23
-
-
39749132831
-
Full Correlation Analysis of Conformational Protein Dynamics
-
Lange, O. F.; Grubmueller, H. Full Correlation Analysis of Conformational Protein Dynamics Proteins: Struct., Funct., Bioinf. 2008, 70 (4) 1294-1312
-
(2008)
Proteins: Struct., Funct., Bioinf.
, vol.70
, Issue.4
, pp. 1294-1312
-
-
Lange, O.F.1
Grubmueller, H.2
-
24
-
-
85162063032
-
Iterative Non-Linear Dimensionality Reduction with Manifold Sculpting
-
Gashler, M.; Ventura, D.; Martinez, T. Iterative Non-Linear Dimensionality Reduction with Manifold Sculpting Adv. Neural Inf. Process. Syst. 2008, 20, 513-520
-
(2008)
Adv. Neural Inf. Process. Syst.
, vol.20
, pp. 513-520
-
-
Gashler, M.1
Ventura, D.2
Martinez, T.3
-
26
-
-
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 (12) 124116
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.12
, pp. 124116
-
-
Rohrdanz, M.A.1
Zheng, W.2
Maggioni, M.3
Clementi, C.4
-
27
-
-
34047253345
-
A Lattice Protein with an Amyloidogenic Latent State: Stability and Folding Kinetics
-
Palyanov, A. Y.; Krivov, S. V.; Karplus, M.; Chekmarev, S. F. A Lattice Protein with an Amyloidogenic Latent State: Stability and Folding Kinetics J. Phys. Chem. B 2007, 111 (10) 2675-2687
-
(2007)
J. Phys. Chem. B
, vol.111
, Issue.10
, pp. 2675-2687
-
-
Palyanov, A.Y.1
Krivov, S.V.2
Karplus, M.3
Chekmarev, S.F.4
-
28
-
-
58549104541
-
Folding Energy Landscape and Network Dynamics of Small Globular Proteins
-
Hori, N.; Chikenji, G.; Berry, R. S.; Takada, D. Folding Energy Landscape and Network Dynamics of Small Globular Proteins Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (1) 73-78
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, Issue.1
, pp. 73-78
-
-
Hori, N.1
Chikenji, G.2
Berry, R.S.3
Takada, D.4
-
29
-
-
0034718553
-
Folding Simulations of a Three-Stranded Antiparallel Beta-Sheet Peptide
-
Ferrara, P.; Caflisch, A. Folding Simulations of a Three-Stranded Antiparallel Beta-Sheet Peptide Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (20) 10780-10785
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, Issue.20
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
30
-
-
79960377563
-
Probing the Folding of Mini-Protein Beta3s by Two- Dimensional Infrared Spectroscopy; Simulation Study
-
Marai, C. N.; Mukamel, S.; Wang, J. Probing the Folding of Mini-Protein Beta3s by Two- Dimensional Infrared Spectroscopy; Simulation Study BMC Biophys. 2010, 3 (1) 8
-
(2010)
BMC Biophys.
, vol.3
, Issue.1
, pp. 8
-
-
Marai, C.N.1
Mukamel, S.2
Wang, J.3
-
31
-
-
77952683491
-
Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a Beta-Sheet Miniprotein
-
Qi, B.; Muff, S.; Caflisch, A.; Dinner, A. R. Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a Beta-Sheet Miniprotein J. Phys. Chem. B 2010, 114 (20) 6979-6989
-
(2010)
J. Phys. Chem. B
, vol.114
, Issue.20
, pp. 6979-6989
-
-
Qi, B.1
Muff, S.2
Caflisch, A.3
Dinner, A.R.4
-
32
-
-
0029970338
-
Evolutionary Optimization in Quantitative Structure-Activity Relationship: An Application of Genetic Neural Networks
-
So, S. S.; Karplus, M. Evolutionary Optimization in Quantitative Structure-Activity Relationship: An Application of Genetic Neural Networks J. Med. Chem. 1996, 39 (7) 1521-1530
-
(1996)
J. Med. Chem.
, vol.39
, Issue.7
, pp. 1521-1530
-
-
So, S.S.1
Karplus, M.2
-
33
-
-
49149126925
-
Folding Pathways and Rates for the Three-Stranded Beta-Sheet Peptide Beta3s Using Discrete Path Sampling
-
Carr, J. M.; Wales, D. J. Folding Pathways and Rates for the Three-Stranded Beta-Sheet Peptide Beta3s Using Discrete Path Sampling J. Phys. Chem. B 2008, 112 (29) 8760-8769
-
(2008)
J. Phys. Chem. B
, vol.112
, Issue.29
, pp. 8760-8769
-
-
Carr, J.M.1
Wales, D.J.2
-
34
-
-
4143090730
-
The Protein Folding Network
-
Rao, F.; Caflisch, A. The Protein Folding Network J. Mol. Biol. 2004, 342 (1) 299-306
-
(2004)
J. Mol. Biol.
, vol.342
, Issue.1
, pp. 299-306
-
-
Rao, F.1
Caflisch, A.2
-
35
-
-
39749156392
-
Kinetic Analysis of Molecular Dynamics Simulations Reveals Changes in the Denatured State and Switch of Folding Pathways upon Single-Point Mutation of a Beta-Sheet Miniprotein
-
Muff, S.; Caflisch, A. Kinetic Analysis of Molecular Dynamics Simulations Reveals Changes in the Denatured State and Switch of Folding Pathways upon Single-Point Mutation of a Beta-Sheet Miniprotein Proteins: Struct., Funct., Bioinf. 2008, 70 (4) 1185-1195
-
(2008)
Proteins: Struct., Funct., Bioinf.
, vol.70
, Issue.4
, pp. 1185-1195
-
-
Muff, S.1
Caflisch, A.2
-
36
-
-
63649158782
-
ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations
-
Muff, S.; Caflisch, A. ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations J. Phys. Chem. B 2009, 113 (10) 3218-3226
-
(2009)
J. Phys. Chem. B
, vol.113
, Issue.10
, pp. 3218-3226
-
-
Muff, S.1
Caflisch, A.2
-
37
-
-
63649158574
-
Identification of the Protein Folding Transition State from Molecular Dynamics Trajectories
-
Muff, S.; Caflisch, A. Identification of the Protein Folding Transition State from Molecular Dynamics Trajectories J. Chem. Phys. 2009, 130 (12) 125104
-
(2009)
J. Chem. Phys.
, vol.130
, Issue.12
, pp. 125104
-
-
Muff, S.1
Caflisch, A.2
-
38
-
-
49149121255
-
One-Dimensional Barrier-Preserving Free-Energy Projections of a Beta-Sheet Miniprotein: New Insights into the Folding Process
-
Krivov, S. V.; Muff, S.; Caflisch, A.; Karplus, M. One-Dimensional Barrier-Preserving Free-Energy Projections of a Beta-Sheet Miniprotein: New Insights into the Folding Process J. Phys. Chem. B 2008, 112 (29) 8701-8714
-
(2008)
J. Phys. Chem. B
, vol.112
, Issue.29
, pp. 8701-8714
-
-
Krivov, S.V.1
Muff, S.2
Caflisch, A.3
Karplus, M.4
-
39
-
-
0001563395
-
On the Transition Coordinate for Protein Folding
-
Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, I. E. On the Transition Coordinate for Protein Folding J. Chem. Phys. 1998, 108 (1) 334-350
-
(1998)
J. Chem. Phys.
, vol.108
, Issue.1
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, I.E.5
-
40
-
-
34548098593
-
Estimation of Protein Folding Probability from Equilibrium Simulations
-
Rao, F.; Settani, G.; Guarnera, E.; Caflisch, A. Estimation of Protein Folding Probability from Equilibrium Simulations J. Chem. Phys. 2005, 122 (18) 184901
-
(2005)
J. Chem. Phys.
, vol.122
, Issue.18
, pp. 184901
-
-
Rao, F.1
Settani, G.2
Guarnera, E.3
Caflisch, A.4
-
41
-
-
33745744079
-
Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates
-
Snow, C. D.; Rhee, Y. M.; Pande, V. S. Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates Biophys. J. 2006, 91 (1) 14-24
-
(2006)
Biophys. J.
, vol.91
, Issue.1
, pp. 14-24
-
-
Snow, C.D.1
Rhee, Y.M.2
Pande, V.S.3
-
42
-
-
0043268848
-
Reaction Paths Based on Mean First-Passage Times
-
Park, S.; Sener, M. K.; Lu, D. Y.; Schulten, K. Reaction Paths Based on Mean First-Passage Times J. Chem. Phys. 2003, 119 (3) 1313-1319
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.3
, pp. 1313-1319
-
-
Park, S.1
Sener, M.K.2
Lu, D.Y.3
Schulten, K.4
-
43
-
-
80455127024
-
Delineation of Folding Pathways of a Beta-Sheet Miniprotein
-
Zheng, W.; Qi, B.; Rohrdanz, M. A.; Caflisch, A.; Dinner, A. R.; Clementi, C. Delineation of Folding Pathways of a Beta-Sheet Miniprotein J. Phys. Chem. B 2011, 115 (44) 13065-13074
-
(2011)
J. Phys. Chem. B
, vol.115
, Issue.44
, pp. 13065-13074
-
-
Zheng, W.1
Qi, B.2
Rohrdanz, M.A.3
Caflisch, A.4
Dinner, A.R.5
Clementi, C.6
-
44
-
-
40749090023
-
Hydrodynamic Description of Protein Folding
-
Chekmarev, S. F.; Palyanov, A. Y.; Karplus, M. Hydrodynamic Description of Protein Folding Phys. Rev. Lett. 2008, 100 (1) 018107
-
(2008)
Phys. Rev. Lett.
, vol.100
, Issue.1
, pp. 018107
-
-
Chekmarev, S.F.1
Palyanov, A.Y.2
Karplus, M.3
-
45
-
-
70349284778
-
Folding of a SH3 Domain: Standard and "hydrodynamic" Analyses
-
Kalgin, I. V.; Karplus, M.; Chekmarev, S. F. Folding of a SH3 Domain: Standard and "Hydrodynamic" Analyses J. Phys. Chem. B 2009, 113 (38) 12759-12772
-
(2009)
J. Phys. Chem. B
, vol.113
, Issue.38
, pp. 12759-12772
-
-
Kalgin, I.V.1
Karplus, M.2
Chekmarev, S.F.3
-
46
-
-
79951693864
-
Turbulent Phenomena in Protein Folding
-
Kalgin, I. V.; Chekmarev, S. F. Turbulent Phenomena in Protein Folding Phys. Rev. E 2011, 83 (1) 011920
-
(2011)
Phys. Rev. e
, vol.83
, Issue.1
, pp. 011920
-
-
Kalgin, I.V.1
Chekmarev, S.F.2
-
47
-
-
0032917075
-
De novo Design of a Monomeric Three-Stranded Antiparallel Beta-Sheet
-
De Alba, E.; Santoro, J.; Rico, M.; Jiménez, M. De novo Design of a Monomeric Three-Stranded Antiparallel Beta-Sheet Protein Sci. 1999, 8 (4) 854-865
-
(1999)
Protein Sci.
, vol.8
, Issue.4
, pp. 854-865
-
-
De Alba, E.1
Santoro, J.2
Rico, M.3
Jiménez, M.4
-
48
-
-
0000036869
-
Simulation of Activation Free Energies in Molecular Systems
-
Neria, E.; Fischer, S.; Karplus, M. Simulation of Activation Free Energies in Molecular Systems J. Chem. Phys. 1996, 105 (5) 1902-1921
-
(1996)
J. Chem. Phys.
, vol.105
, Issue.5
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
49
-
-
0036138028
-
Evaluation of a Fast Implicit Solvent Model for Molecular Dynamics Simulations
-
Ferrara, P.; Apostolakis, J.; Caflisch, A. Evaluation of a Fast Implicit Solvent Model for Molecular Dynamics Simulations Proteins: Struct., Funct., Genet. 2002, 46 (1) 24-33
-
(2002)
Proteins: Struct., Funct., Genet.
, vol.46
, Issue.1
, pp. 24-33
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
50
-
-
0001767031
-
Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations
-
Ferrara, P.; Apostolakis, J.; Caflisch, A. Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations J. Phys. Chem. B 2000, 104 (20) 5000-5010
-
(2000)
J. Phys. Chem. B
, vol.104
, Issue.20
, pp. 5000-5010
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
51
-
-
14144255497
-
Phi-Value Analysis by Molecular Dynamics Simulations of Reversible Folding
-
Settanni, G.; Rao, F.; Caflisch, A. Phi-Value Analysis by Molecular Dynamics Simulations of Reversible Folding Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (3) 628-633
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, Issue.3
, pp. 628-633
-
-
Settanni, G.1
Rao, F.2
Caflisch, A.3
-
52
-
-
0033624685
-
Fast Kinetics and Mechanisms in Protein Folding
-
Eaton, W. A.; Munoz, V.; Hagen, J.; Jas, S. G. S.; Lapidus, L. J.; Henry, E. R.; Hofrichter, J. Fast Kinetics and Mechanisms in Protein Folding Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 327-359
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 327-359
-
-
Eaton, W.A.1
Munoz, V.2
Hagen, J.3
Jas, S.G.S.4
Lapidus, L.J.5
Henry, E.R.6
Hofrichter, J.7
-
53
-
-
0037093655
-
Weak Temperature Dependence of the Free Energy Surface and Folding Pathways of Structured Peptides
-
Cavalli, A.; Ferrara, P.; Caflisch, A. Weak Temperature Dependence of the Free Energy Surface and Folding Pathways of Structured Peptides Proteins: Struct., Funct., Genet. 2002, 47 (3) 305-314
-
(2002)
Proteins: Struct., Funct., Genet.
, vol.47
, Issue.3
, pp. 305-314
-
-
Cavalli, A.1
Ferrara, P.2
Caflisch, A.3
-
54
-
-
0000127140
-
Method for Estimating the Configurational Entropy of Macromolecules
-
Karplus, M.; Kushick, J. Method for Estimating the Configurational Entropy of Macromolecules Macromolecules 1981, 14 (2) 325-332
-
(1981)
Macromolecules
, vol.14
, Issue.2
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.2
-
55
-
-
0035998835
-
Model-Based Clustering, Discriminant Analysis, and Density Estimation
-
Fraley, C.; Raftery, A. E. Model-Based Clustering, Discriminant Analysis, and Density Estimation J. Am. Stat. Assoc. 2002, 97 (458) 611-631
-
(2002)
J. Am. Stat. Assoc.
, vol.97
, Issue.458
, pp. 611-631
-
-
Fraley, C.1
Raftery, A.E.2
-
56
-
-
85067780821
-
-
http://www.stat.washington.edu/fraley/mclust/.
-
-
-
-
57
-
-
0036174712
-
Continuum Secondary Structure Captures Protein Flexibility
-
Andersen, C. A.; Palmer, A. G.; Brunak, S.; Rost, B. Continuum Secondary Structure Captures Protein Flexibility Structure 2002, 10 (2) 175-184
-
(2002)
Structure
, vol.10
, Issue.2
, pp. 175-184
-
-
Andersen, C.A.1
Palmer, A.G.2
Brunak, S.3
Rost, B.4
-
58
-
-
35748935079
-
Wordom: A Program for Efficient Analysis of Molecular Dynamics Simulations
-
Seeber, M.; Cecchini, M.; Rao, F.; Settanni, G.; Caflisch, A. Wordom: a Program for Efficient Analysis of Molecular Dynamics Simulations Bioinformatics 2007, 23 (19) 2625-2627
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2625-2627
-
-
Seeber, M.1
Cecchini, M.2
Rao, F.3
Settanni, G.4
Caflisch, A.5
-
60
-
-
0029686346
-
An Analysis of 3D Particle Path Integration Algorithms
-
Darmofal, D. L.; Haimes, R. An Analysis of 3D Particle Path Integration Algorithms J. Comput. Phys. 1996, 123 (1) 182-195
-
(1996)
J. Comput. Phys.
, vol.123
, Issue.1
, pp. 182-195
-
-
Darmofal, D.L.1
Haimes, R.2
-
61
-
-
85067773929
-
Visualization of 3-D Vector Fields: Variations on a Stream
-
(92-0074).
-
Darmofal, D. L.; Haimes, R. Visualization of 3-D Vector Fields: Variations on a Stream. AIAA Pap. (92-0074).
-
AIAA Pap.
-
-
Darmofal, D.L.1
Haimes, R.2
-
62
-
-
84862180821
-
Free Energy Guided Sampling
-
Zhou, T.; Caflisch, A. Free Energy Guided Sampling J. Chem. Theory Comput. 2012, 8 (6) 2134-2140
-
(2012)
J. Chem. Theory Comput.
, vol.8
, Issue.6
, pp. 2134-2140
-
-
Zhou, T.1
Caflisch, A.2
-
63
-
-
79951523268
-
Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations
-
Zheng, W.; Gallicchio, E.; Deng, N.; Andrec, M.; Levy, R. M. Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations J. Phys. Chem. B 2011, 115 (6) 1512-1523
-
(2011)
J. Phys. Chem. B
, vol.115
, Issue.6
, pp. 1512-1523
-
-
Zheng, W.1
Gallicchio, E.2
Deng, N.3
Andrec, M.4
Levy, R.M.5
-
64
-
-
66849091890
-
Reactive Flux and Folding Pathways in Network Models of Coarse-Grained Protein Dynamics
-
Berezhkovskii, A.; Hummer, G.; Szabo, A. Reactive Flux and Folding Pathways in Network Models of Coarse-Grained Protein Dynamics J. Chem. Phys. 2009, 130 (20) 205102
-
(2009)
J. Chem. Phys.
, vol.130
, Issue.20
, pp. 205102
-
-
Berezhkovskii, A.1
Hummer, G.2
Szabo, A.3
-
65
-
-
70450255797
-
Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations
-
Noé, F.; Schütte, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (45) 19011-19016
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, Issue.45
, pp. 19011-19016
-
-
Noé, F.1
Schütte, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
|