-
1
-
-
34247953814
-
More is different
-
Anderson, P. More is Different Science 1972, 177, 393-396
-
(1972)
Science
, vol.177
, pp. 393-396
-
-
Anderson, P.1
-
2
-
-
58149232341
-
Navigability of complex networks
-
Boguñá, M.; Krioukov, D.; Claffy, K. Navigability of Complex Networks Nat. Phys. 2008, 5, 74-80
-
(2008)
Nat. Phys.
, vol.5
, pp. 74-80
-
-
Boguñá, M.1
Krioukov, D.2
Claffy, K.3
-
3
-
-
60749085416
-
Navigating ultrasmall worlds in ultrashort time
-
Boguñá, M.; Krioukov, D. Navigating Ultrasmall Worlds in Ultrashort Time Phys. Rev. Lett. 2009, 102, 58701
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 58701
-
-
Boguñá, M.1
Krioukov, D.2
-
4
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder, H.; Sligar, S.; Wolynes, P. The Energy Landscapes and Motions of Proteins Science 1991, 254, 1598-1603
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.2
Wolynes, P.3
-
5
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern, D.; Zuiderweg, E. R. The Role of Dynamics in Allosteric Regulation Curr. Opin. Struct. Biol. 2003, 13, 748-577
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 748-577
-
-
Kern, D.1
Zuiderweg, E.R.2
-
6
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser, E. Z. Intrinsic Dynamics of an Enzyme Underlies Catalysis Nature 2005, 438, 117-121
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
-
7
-
-
40849097646
-
Free-energy landscape of enzyme catalysis
-
Benkovic, S. J.; Hammes, G. G.; Hammes-Schiffer, S. Free-Energy Landscape of Enzyme Catalysis Biochemistry 2008, 47, 3317-3321
-
(2008)
Biochemistry
, vol.47
, pp. 3317-3321
-
-
Benkovic, S.J.1
Hammes, G.G.2
Hammes-Schiffer, S.3
-
8
-
-
33748781457
-
The dynamic energy landscape of dihydrofolate reductase catalysis
-
Boehr, D. D.; McElheny, D; Dyson, H. J.; Wright, P. E. The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis Science 2006, 313, 1638-1642
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
9
-
-
39149087014
-
Protein folding studied by single-molecule fret
-
Schuler, B; Eaton, W. A. Protein Folding Studied by Single-Molecule FRET Curr. Opin. Struct. Biol. 2008, 18, 16-26
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 16-26
-
-
Schuler, B.1
Eaton, W.A.2
-
10
-
-
50149111314
-
Shoot-and-trap: Use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography
-
Colletier, J. P. Shoot-and-Trap: Use of Specific X-ray Damage to Study Structural Protein Dynamics by Temperature-Controlled Cryo-crystallography Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11742-11747
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 11742-11747
-
-
Colletier, J.P.1
-
11
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du, R.; Pande, V.; Grosberg, A.; Tanaka, T.; Shakhnovich, E. On the transition coordinate for protein folding J. Chem. Phys. 1998, 108, 334-350
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.2
Grosberg, A.3
Tanaka, T.4
Shakhnovich, E.5
-
12
-
-
0032005143
-
Pathways for protein folding: Is a new view needed?
-
Pande, V.; Grosberg, A.; Tanaka, T.; Rokhsar, D. Pathways for Protein Folding: Is a New View Needed? Curr. Opin. Struct. Biol. 1998, 8, 68-79
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 68-79
-
-
Pande, V.1
Grosberg, A.2
Tanaka, T.3
Rokhsar, D.4
-
13
-
-
33846382040
-
How complex is the dynamics of peptide folding?
-
Hegger, R.; Altis, A.; Nguyen, P.; Stock, G. How Complex Is the Dynamics of Peptide Folding? Phys. Rev. Lett. 2007, 98, 28102
-
(2007)
Phys. Rev. Lett.
, vol.98
, pp. 28102
-
-
Hegger, R.1
Altis, A.2
Nguyen, P.3
Stock, G.4
-
14
-
-
67249126712
-
How adequate are one-and two-dimensional free energy landscapes for protein folding dynamics?
-
Maisuradze, G.; Liwo, A.; Scheraga, H. How Adequate Are One-and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics? Phys. Rev. Lett. 2009, 102, 238102
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 238102
-
-
Maisuradze, G.1
Liwo, A.2
Scheraga, H.3
-
15
-
-
19044389971
-
Network topology of a potential energy landscape: A static scale-free network
-
Doye, J. Network Topology of a Potential Energy Landscape: A Static Scale-Free Network Phys. Rev. Lett. 2002, 88, 238701
-
(2002)
Phys. Rev. Lett.
, vol.88
, pp. 238701
-
-
Doye, J.1
-
16
-
-
0344236155
-
The free energy landscape and dynamics of met-enkephalin
-
Evans, D.; Wales, D. the Free Energy Landscape and Dynamics of Met-enkephalin J. Chem. Phys. 2003, 119, 9947
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 9947
-
-
Evans, D.1
Wales, D.2
-
17
-
-
4143090730
-
The protein folding network
-
Rao, F.; Caflisch, A. The Protein Folding Network J. Mol. Biol. 2004, 342, 299-306
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 299-306
-
-
Rao, F.1
Caflisch, A.2
-
18
-
-
6944235051
-
Hidden complexity of free energy surfaces for peptide (protein) folding
-
Krivov, S.; Karplus, M. Hidden Complexity of Free Energy Surfaces for Peptide (Protein) Folding Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14766-14770
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 14766-14770
-
-
Krivov, S.1
Karplus, M.2
-
19
-
-
34247339716
-
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
-
Noé, F.; Horenko, I.; Schütte, C.; Smith, J. Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States J. Chem. Phys. 2007, 126, 155102
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155102
-
-
Noé, F.1
Horenko, I.2
Schütte, C.3
Smith, J.4
-
20
-
-
32344450229
-
Network and graph analyses of folding free energy surfaces
-
Caflisch, A. Network and Graph Analyses of Folding Free Energy Surfaces Curr. Opin. Struct. Biol. 2006, 16, 71-78
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 71-78
-
-
Caflisch, A.1
-
21
-
-
33846917109
-
Complex network analysis of free-energy landscapes
-
Gfeller, D.; De Los Rios, P.; Caflisch, A.; Rao, F. Complex Network Analysis of Free-Energy Landscapes Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1817-1822
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 1817-1822
-
-
Gfeller, D.1
De Los Rios, P.2
Caflisch, A.3
Rao, F.4
-
22
-
-
44849116304
-
High temperature unfolding simulations of the trpz1 peptide
-
Settanni, G.; Fersht, A. R. High Temperature Unfolding Simulations of the TRPZ1 Peptide Biophys. J. 2008, 94, 4444-4453
-
(2008)
Biophys. J.
, vol.94
, pp. 4444-4453
-
-
Settanni, G.1
Fersht, A.R.2
-
23
-
-
41849097740
-
Src kinase conformational activation: Thermodynamics, pathways, and mechanisms
-
Yang, S.; Roux, B. Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms PLoS Comput. Biol. 2008, 4
-
(2008)
PLoS Comput. Biol.
, pp. 4
-
-
Yang, S.1
Roux, B.2
-
24
-
-
67650886042
-
Exploring the free energy landscape: From dynamics to networks and back
-
Prada-Gracia, D.; Gómez-Gardeñes, J.; Echenique, P.; Falo, F. Exploring the Free Energy Landscape: From Dynamics to Networks and Back PLoS Comput. Biol. 2009, 5, e1000415
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 1000415
-
-
Prada-Gracia, D.1
Gómez-Gardeñes, J.2
Echenique, P.3
Falo, F.4
-
25
-
-
38649113858
-
Multiscale complex network of protein conformational fluctuations in single-molecule time series
-
Li, C. B.; Yang, H.; Komatsuzaki, T. Multiscale Complex Network of Protein Conformational Fluctuations in Single-Molecule Time Series Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 536-541
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 536-541
-
-
Li, C.B.1
Yang, H.2
Komatsuzaki, T.3
-
26
-
-
34248388108
-
Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds
-
Ihalainen, J. A. Folding and Unfolding of a Photoswitchable Peptide from Picoseconds to Microseconds Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 5383-5388
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 5383-5388
-
-
Ihalainen, J.A.1
-
27
-
-
47749149231
-
Alpha-helix folding in the presence of structural constraints
-
Ihalainen, J. A. Alpha-Helix Folding in the Presence of Structural Constraints Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9588-9593
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 9588-9593
-
-
Ihalainen, J.A.1
-
28
-
-
58149461531
-
Partition of networks into basins of attraction
-
Carmi, S.; Krapivsky, P.; Ben-Avraham, D. Partition of Networks into Basins of Attraction Phys. Rev. E 2008, 78, 066111
-
(2008)
Phys. Rev. e
, vol.78
, pp. 066111
-
-
Carmi, S.1
Krapivsky, P.2
Ben-Avraham, D.3
-
29
-
-
1942424168
-
Jamming is limited in scale-free systems
-
Toroczkai, Z.; Bassler, K. Jamming is Limited in Scale-Free Systems Nature 2004, 716
-
(2004)
Nature
, pp. 716
-
-
Toroczkai, Z.1
Bassler, K.2
-
30
-
-
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, 12689-12698
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12689-12698
-
-
Krivov, S.V.1
Karplus, M.2
-
31
-
-
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, 8701-8714
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 8701-8714
-
-
Krivov, S.V.1
Muff, S.2
Caflisch, A.3
Karplus, M.4
-
32
-
-
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, 125104
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 125104
-
-
Muff, S.1
Caflisch, A.2
-
34
-
-
34247338100
-
Automatic discovery of metastable states for the construction of markov models of macromolecular conformational dynamics
-
Chodera, J.; Singhal, N.; Pande, V.; Dill, K.; Swope, W. Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics J. Chem. Phys. 2007, 126, 155101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.1
Singhal, N.2
Pande, V.3
Dill, K.4
Swope, W.5
-
35
-
-
0033578370
-
The speed limit for protein folding measured by triplet-triplet energy transfer
-
Bieri, O. the Speed Limit for Protein Folding Measured by Triplet-Triplet Energy Transfer Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9597
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 9597
-
-
Bieri, O.1
-
36
-
-
33747623305
-
End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation
-
Möglich, A.; Joder, K.; Kiefhaber, T. End-to-End Distance Distributions and Intrachain Diffusion Constants in Unfolded Polypeptide Chains Indicate Intramolecular Hydrogen Bond Formation Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 12394
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 12394
-
-
Möglich, A.1
Joder, K.2
Kiefhaber, T.3
-
37
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R. CHARMM: a Program for Macromolecular Energy, Minimization, And Dynamics Calculations J. Comput. Chem. 1983, 4, 187-217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
-
38
-
-
40549111613
-
FACTS: Fast analytical continuum treatment of solvation
-
Haberthur, U.; Caflisch, A. FACTS: Fast Analytical Continuum Treatment of Solvation J. Comput. Chem. 2008, 29, 701-715
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 701-715
-
-
Haberthur, U.1
Caflisch, A.2
-
39
-
-
4243492437
-
Hidden structure in liquids
-
Stillinger, F.; Weber, T. Hidden Structure in Liquids Phys. Rev. A 1982, 25, 978-989
-
(1982)
Phys. Rev. A
, vol.25
, pp. 978-989
-
-
Stillinger, F.1
Weber, T.2
-
40
-
-
4243264015
-
Dynamics of structural transitions in liquids
-
Stillinger, F.; Weber, T. Dynamics of Structural Transitions in Liquids Phys. Rev. A 1983, 28, 2408-2416
-
(1983)
Phys. Rev. A
, vol.28
, pp. 2408-2416
-
-
Stillinger, F.1
Weber, T.2
-
41
-
-
0038029818
-
Glass transition in an off-lattice protein model studied by molecular dynamics simulations
-
Baumketner, A.; Shea, J. E.; Hiwatari, Y. Glass Transition in an off-Lattice Protein Model Studied by Molecular Dynamics Simulations Phys. Rev. E 2003, 67, 011912
-
(2003)
Phys. Rev. e
, vol.67
, pp. 011912
-
-
Baumketner, A.1
Shea, J.E.2
Hiwatari, Y.3
-
42
-
-
34047248673
-
Inherent structure analysis of protein folding
-
Kim, J.; Keyes, T. Inherent Structure Analysis of Protein Folding J. Phys. Chem. B 2007, 111, 2647-2657
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 2647-2657
-
-
Kim, J.1
Keyes, T.2
-
43
-
-
33645773437
-
The inherent structure landscape of a protein
-
Nakagawa, N.; Peyrard, M. The Inherent Structure Landscape of a Protein Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 5279-5284
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 5279-5284
-
-
Nakagawa, N.1
Peyrard, M.2
-
44
-
-
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, 2625-2627
-
(2007)
Bioinformatics
, vol.23
, pp. 2625-2627
-
-
Seeber, M.1
Cecchini, M.2
Rao, F.3
Settanni, G.4
Caflisch, A.5
|