-
1
-
-
61349179602
-
The structural dynamics of macromolecular processes
-
Russel D., Lasker K., Phillips J., Schneidman-Duhovny D., Velazquez-Muriel J.A., Sali A. The structural dynamics of macromolecular processes. Curr Opin Cell Biol 2009, 21:97-108.
-
(2009)
Curr Opin Cell Biol
, vol.21
, pp. 97-108
-
-
Russel, D.1
Lasker, K.2
Phillips, J.3
Schneidman-Duhovny, D.4
Velazquez-Muriel, J.A.5
Sali, A.6
-
2
-
-
39149100599
-
Coarse-grained models of protein folding: toy models or predictive tools?
-
Clementi C. Coarse-grained models of protein folding: toy models or predictive tools?. Curr Opin Struct Biol 2008, 18:10-15.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 10-15
-
-
Clementi, C.1
-
5
-
-
77949634796
-
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins
-
Bahar I., Lezon T.R., Bakan A., Shrivastava I.H. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010, 110:1463-1497.
-
(2010)
Chem Rev
, vol.110
, pp. 1463-1497
-
-
Bahar, I.1
Lezon, T.R.2
Bakan, A.3
Shrivastava, I.H.4
-
7
-
-
77952938726
-
Global dynamics of proteins: bridging between structure and function
-
Bahar I., Lezon T.R., Yang L.W., Eyal E. Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys 2010, 39:23-42.
-
(2010)
Annu Rev Biophys
, vol.39
, pp. 23-42
-
-
Bahar, I.1
Lezon, T.R.2
Yang, L.W.3
Eyal, E.4
-
8
-
-
49649084492
-
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms
-
Okazaki K., Takada S. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc Natl Acad Sci USA 2008, 105:11182-11187.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 11182-11187
-
-
Okazaki, K.1
Takada, S.2
-
9
-
-
70149090164
-
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
-
Bakan A., Bahar I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci USA 2009, 106:14349-14354.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
10
-
-
62549167040
-
Ligand-induced global transitions in the catalytic domain of protein kinase A
-
Hyeon C., Jennings P.A., Adams J.A., Onuchic J.N. Ligand-induced global transitions in the catalytic domain of protein kinase A. Proc Natl Acad Sci USA 2009, 106:3023-3028.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 3023-3028
-
-
Hyeon, C.1
Jennings, P.A.2
Adams, J.A.3
Onuchic, J.N.4
-
11
-
-
0035427398
-
Protein flexibility predictions using graph theory
-
Jacobs D.J., Rader A.J., Thorpe M.F., Kuhn L.A. Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 2001, 44:150-165.
-
(2001)
Proteins: Struct Funct Genet
, vol.44
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.J.2
Thorpe, M.F.3
Kuhn, L.A.4
-
12
-
-
27744471408
-
Constrained geometric simulation of diffusive motion in proteins
-
Wells S., Menor S., Hespenheide B., Thorpe M.F. Constrained geometric simulation of diffusive motion in proteins. Phys Biol 2005, 2:S127-S136.
-
(2005)
Phys Biol
, vol.2
-
-
Wells, S.1
Menor, S.2
Hespenheide, B.3
Thorpe, M.F.4
-
13
-
-
36549005182
-
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian
-
Moritsugu K., Smith J.C. Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J 2007, 93:3460-3469.
-
(2007)
Biophys J
, vol.93
, pp. 3460-3469
-
-
Moritsugu, K.1
Smith, J.C.2
-
14
-
-
35748982413
-
Geometry-based sampling of conformational transitions in proteins
-
Seeliger D., Haas J., de Groot B.L. Geometry-based sampling of conformational transitions in proteins. Structure 2007, 15:1482-1492.
-
(2007)
Structure
, vol.15
, pp. 1482-1492
-
-
Seeliger, D.1
Haas, J.2
de Groot, B.L.3
-
16
-
-
77957948190
-
Generating stereochemically acceptable protein pathways
-
Farrell D.W., Speranskiy K., Thorpe M.F. Generating stereochemically acceptable protein pathways. Proteins 2010, 78:2908-2921.
-
(2010)
Proteins
, vol.78
, pp. 2908-2921
-
-
Farrell, D.W.1
Speranskiy, K.2
Thorpe, M.F.3
-
17
-
-
76749123486
-
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations
-
Seeliger D., de Groot B.L. Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol 2010, 6:e1000634.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Seeliger, D.1
de Groot, B.L.2
-
18
-
-
76249128215
-
Theory and normal-mode analysis of change in protein vibrational dynamics on ligand binding
-
Moritsugu K., Njunda B.M., Smith J.C. Theory and normal-mode analysis of change in protein vibrational dynamics on ligand binding. J Phys Chem B 2010, 114:1479-1485.
-
(2010)
J Phys Chem B
, vol.114
, pp. 1479-1485
-
-
Moritsugu, K.1
Njunda, B.M.2
Smith, J.C.3
-
19
-
-
1542285840
-
Network rigidity at finite temperature: relationships between thermodynamics stability, the nonadditivity of entropy, and cooperativity in molecular systems
-
Jacobs D.J., Dallakyan S., Wood G.G., Heckathorne A. Network rigidity at finite temperature: relationships between thermodynamics stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys Rev E 2003, 68:61109-61122.
-
(2003)
Phys Rev E
, vol.68
, pp. 61109-61122
-
-
Jacobs, D.J.1
Dallakyan, S.2
Wood, G.G.3
Heckathorne, A.4
-
20
-
-
41449099769
-
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
-
Jolley C.C., Wells S.A., Fromme P., Thorpe M.F. Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. Biophys J 2008, 94:1613-1621.
-
(2008)
Biophys J
, vol.94
, pp. 1613-1621
-
-
Jolley, C.C.1
Wells, S.A.2
Fromme, P.3
Thorpe, M.F.4
-
21
-
-
34547474332
-
The MARTINI force field: coarse grained model for biomolecular simulations
-
Marrink S.J., Risselada H.J., Yefimov S., Tieleman D.P., de Vries A.H. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 2007, 111:7812-7824.
-
(2007)
J Phys Chem B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
de Vries, A.H.5
-
22
-
-
61649098586
-
Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding
-
Fulle S., Gohlke H. Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol 2009, 387:502-517.
-
(2009)
J Mol Biol
, vol.387
, pp. 502-517
-
-
Fulle, S.1
Gohlke, H.2
-
23
-
-
66149167201
-
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling
-
Kurkcuoglu O., Kurkcuoglu Z., Doruker P., Jernigan R.L. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins 2009, 75:837-845.
-
(2009)
Proteins
, vol.75
, pp. 837-845
-
-
Kurkcuoglu, O.1
Kurkcuoglu, Z.2
Doruker, P.3
Jernigan, R.L.4
-
24
-
-
33845204189
-
Stability and dynamics of virus capsids described by coarse-grained modeling
-
Arkhipov A., Freddolino P.L., Schulten K. Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 2006, 14:1767-1777.
-
(2006)
Structure
, vol.14
, pp. 1767-1777
-
-
Arkhipov, A.1
Freddolino, P.L.2
Schulten, K.3
-
25
-
-
72049092011
-
Membrane-bending mechanism of amphiphysin N-BAR domains
-
Arkhipov A., Yin Y., Schulten K. Membrane-bending mechanism of amphiphysin N-BAR domains. Biophys J 2009, 97:2727-2735.
-
(2009)
Biophys J
, vol.97
, pp. 2727-2735
-
-
Arkhipov, A.1
Yin, Y.2
Schulten, K.3
-
26
-
-
64749105956
-
Hybrid coarse-graining approach for lipid bilayers at large length and time scales
-
Ayton G.S., Voth G.A. Hybrid coarse-graining approach for lipid bilayers at large length and time scales. J Phys Chem B 2009, 113:4413-4424.
-
(2009)
J Phys Chem B
, vol.113
, pp. 4413-4424
-
-
Ayton, G.S.1
Voth, G.A.2
-
27
-
-
70350233625
-
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales
-
Ayton G.S., Lyman E., Voth G.A. Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discuss 2010, 144:347-357.
-
(2010)
Faraday Discuss
, vol.144
, pp. 347-357
-
-
Ayton, G.S.1
Lyman, E.2
Voth, G.A.3
-
28
-
-
33847209200
-
Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints
-
Murtola T., Falck E., Karttunen M., Vattulainen I. Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints. J Chem Phys 2007, 126:075101.
-
(2007)
J Chem Phys
, vol.126
, pp. 075101
-
-
Murtola, T.1
Falck, E.2
Karttunen, M.3
Vattulainen, I.4
-
29
-
-
62349124337
-
Multiscale modeling of emergent materials: biological and soft matter
-
Murtola T., Bunker A., Vattulainen I., Deserno M., Karttunen M. Multiscale modeling of emergent materials: biological and soft matter. Phys Chem Chem Phys 2009, 11:1869-1892.
-
(2009)
Phys Chem Chem Phys
, vol.11
, pp. 1869-1892
-
-
Murtola, T.1
Bunker, A.2
Vattulainen, I.3
Deserno, M.4
Karttunen, M.5
-
30
-
-
33847094275
-
Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins
-
Rojas A.V., Liwo A., Scheraga H.A. Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B 2007, 111:293-309.
-
(2007)
J Phys Chem B
, vol.111
, pp. 293-309
-
-
Rojas, A.V.1
Liwo, A.2
Scheraga, H.A.3
-
31
-
-
14544291957
-
A multiscale coarse-graining method for biomolecular systems
-
Izvekov S., Voth G.A. A multiscale coarse-graining method for biomolecular systems. J Phys Chem B 2005, 109:2469-2473.
-
(2005)
J Phys Chem B
, vol.109
, pp. 2469-2473
-
-
Izvekov, S.1
Voth, G.A.2
-
32
-
-
54949109484
-
The relative entropy is fundamental to multiscale and inverse thermodynamic problems
-
Shell M.S. The relative entropy is fundamental to multiscale and inverse thermodynamic problems. J Chem Phys 2008, 129:144108.
-
(2008)
J Chem Phys
, vol.129
, pp. 144108
-
-
Shell, M.S.1
-
33
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
-
Miyazawa S., Jernigan R.L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
34
-
-
65949085330
-
Another look at the conditions for the extraction of protein knowledge-based potentials
-
Betancourt M.R. Another look at the conditions for the extraction of protein knowledge-based potentials. Proteins 2009, 76:72-85.
-
(2009)
Proteins
, vol.76
, pp. 72-85
-
-
Betancourt, M.R.1
-
35
-
-
65949084921
-
Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
-
Betancourt M.R., Omovie S.J. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields. J Chem Phys 2009, 130:195103.
-
(2009)
J Chem Phys
, vol.130
, pp. 195103
-
-
Betancourt, M.R.1
Omovie, S.J.2
-
36
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
-
Taketomi H., Ueda Y., Go N. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 1975, 7:445-459.
-
(1975)
Int J Pept Protein Res
, vol.7
, pp. 445-459
-
-
Taketomi, H.1
Ueda, Y.2
Go, N.3
-
37
-
-
63449129633
-
Insights from coarse-grained go models for protein folding and dynamics
-
Hills R.D., Brooks C.L. Insights from coarse-grained go models for protein folding and dynamics. Int J Mol Sci 2009, 10:889-905.
-
(2009)
Int J Mol Sci
, vol.10
, pp. 889-905
-
-
Hills, R.D.1
Brooks, C.L.2
-
38
-
-
2342471328
-
Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin
-
Zuckerman D.M. Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin. J Phys Chem B 2004, 108:5127-5137.
-
(2004)
J Phys Chem B
, vol.108
, pp. 5127-5137
-
-
Zuckerman, D.M.1
-
39
-
-
33747065536
-
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations
-
Okazaki K., Koga N., Takada S., Onuchic J.N., Wolynes P.G. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: structure-based molecular dynamics simulations. Proc Natl Acad Sci USA 2006, 103:11844-11849.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 11844-11849
-
-
Okazaki, K.1
Koga, N.2
Takada, S.3
Onuchic, J.N.4
Wolynes, P.G.5
-
40
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter
-
Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter. At Anal Phys Rev Lett 1996, 77:1905-1908.
-
(1996)
At Anal Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
41
-
-
68149141470
-
Protein elastic network models and the ranges of cooperativity
-
Yang L., Song G., Jernigan R.L. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci USA 2009, 106:12347-12352.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 12347-12352
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
42
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar I., Rader A.J. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005, 15:586-592.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
43
-
-
34547666968
-
How well can we understand large-scale protein motions using normal modes of elastic network models?
-
Yang L., Song G., Jernigan R.L. How well can we understand large-scale protein motions using normal modes of elastic network models?. Biophys J 2007, 93:920-929.
-
(2007)
Biophys J
, vol.93
, pp. 920-929
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
44
-
-
21244483843
-
Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity
-
Jacobs D.J., Dallakyan S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophys J 2005, 88:903-915.
-
(2005)
Biophys J
, vol.88
, pp. 903-915
-
-
Jacobs, D.J.1
Dallakyan, S.2
-
45
-
-
6344223617
-
A flexible approach for understanding protein stability
-
Livesay D.R., Dallakyan S., Wood G.G., Jacobs D.J. A flexible approach for understanding protein stability. FEBS Lett 2004, 576:468-476.
-
(2004)
FEBS Lett
, vol.576
, pp. 468-476
-
-
Livesay, D.R.1
Dallakyan, S.2
Wood, G.G.3
Jacobs, D.J.4
-
46
-
-
36749088906
-
Determining the architectures of macromolecular assemblies
-
Alber F., Dokudovskaya S., Veenhoff L.M., Zhang W., Kipper J., Devos D., Suprapto A., Karni-Schmidt O., Williams R., Chait B.T., et al. Determining the architectures of macromolecular assemblies. Nature 2007, 450:683-694.
-
(2007)
Nature
, vol.450
, pp. 683-694
-
-
Alber, F.1
Dokudovskaya, S.2
Veenhoff, L.M.3
Zhang, W.4
Kipper, J.5
Devos, D.6
Suprapto, A.7
Karni-Schmidt, O.8
Williams, R.9
Chait, B.T.10
-
47
-
-
77955388349
-
Integrative structure modeling of macromolecular assemblies from proteomics data
-
Lasker K., Phillips J.L., Russel D., Velazquez-Muriel J., Schneidman-Duhovny D., Tjioe E., Webb B., Schlessinger A., Sali A. Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics 2010, 9:1689-1702.
-
(2010)
Mol Cell Proteomics
, vol.9
, pp. 1689-1702
-
-
Lasker, K.1
Phillips, J.L.2
Russel, D.3
Velazquez-Muriel, J.4
Schneidman-Duhovny, D.5
Tjioe, E.6
Webb, B.7
Schlessinger, A.8
Sali, A.9
-
48
-
-
70349661903
-
Global motions of the nuclear pore complex: insights from elastic network models
-
Lezon T.R., Sali A., Bahar I. Global motions of the nuclear pore complex: insights from elastic network models. PLoS Comput Biol 2009, 5:e1000496.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Lezon, T.R.1
Sali, A.2
Bahar, I.3
-
49
-
-
77955487466
-
Multiscale coarse-graining of the protein energy landscape
-
Hills R.D., Lu L.Y., Voth G.A. Multiscale coarse-graining of the protein energy landscape. PLoS Comput Biol 2010, 6:e100827.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Hills, R.D.1
Lu, L.Y.2
Voth, G.A.3
-
50
-
-
0035902367
-
A coarse grain model for phospholipid simulations
-
Shelley J.C., Shelley M.Y., Reeder R.C., Bandyopadhyay S., Klein M.L. A coarse grain model for phospholipid simulations. J Phys Chem B 2001, 105:4464-4470.
-
(2001)
J Phys Chem B
, vol.105
, pp. 4464-4470
-
-
Shelley, J.C.1
Shelley, M.Y.2
Reeder, R.C.3
Bandyopadhyay, S.4
Klein, M.L.5
-
51
-
-
49449113010
-
The MARTINI coarse-grained force field: extension to proteins
-
Monticelli L., Kandasamy S.K., Periole X., Larson R.G., Tieleman D.P., Marrink S.J. The MARTINI coarse-grained force field: extension to proteins. J Chem Theory Comput 2008, 4:819-834.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.J.6
-
52
-
-
34248159870
-
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics
-
Rueda M., Chacon P., Orozco M. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure 2007, 15:565-575.
-
(2007)
Structure
, vol.15
, pp. 565-575
-
-
Rueda, M.1
Chacon, P.2
Orozco, M.3
-
53
-
-
78049307626
-
Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins
-
Haliloglu T., Gul A., Erman B. Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins. PLoS Comput Biol 2010, 6:e1000845.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Haliloglu, T.1
Gul, A.2
Erman, B.3
-
54
-
-
44949215646
-
Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model
-
Haliloglu T., Seyrek E., Erman B. Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. Phys Rev Lett 2008, 100:228102.
-
(2008)
Phys Rev Lett
, vol.100
, pp. 228102
-
-
Haliloglu, T.1
Seyrek, E.2
Erman, B.3
-
55
-
-
33646742004
-
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
-
Zheng W., Brooks B.R., Thirumalai D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci USA 2006, 103:7664-7669.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 7664-7669
-
-
Zheng, W.1
Brooks, B.R.2
Thirumalai, D.3
-
56
-
-
43349093759
-
Analysis of correlated mutations in HIV-1 protease using spectral clustering
-
Liu Y., Eyal E., Bahar I. Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics 2008, 24:1243-1250.
-
(2008)
Bioinformatics
, vol.24
, pp. 1243-1250
-
-
Liu, Y.1
Eyal, E.2
Bahar, I.3
-
57
-
-
0037764042
-
Molecular dynamics simulations of peptides and proteins with amplified collective motions
-
Zhang Z., Shi Y., Liu H. Molecular dynamics simulations of peptides and proteins with amplified collective motions. Biophys J 2003, 84:3583-3593.
-
(2003)
Biophys J
, vol.84
, pp. 3583-3593
-
-
Zhang, Z.1
Shi, Y.2
Liu, H.3
-
58
-
-
34547649538
-
A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks
-
Essiz S., Coalson R.D. A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks. J Chem Phys 2006, 124:144116.
-
(2006)
J Chem Phys
, vol.124
, pp. 144116
-
-
Essiz, S.1
Coalson, R.D.2
-
59
-
-
58149161251
-
Systematic multiscale parameterization of heterogeneous elastic network models of proteins
-
Lyman E., Pfaendtner J., Voth G.A. Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys J 2008, 95:4183-4192.
-
(2008)
Biophys J
, vol.95
, pp. 4183-4192
-
-
Lyman, E.1
Pfaendtner, J.2
Voth, G.A.3
-
60
-
-
70349336348
-
The energy profiles of atomic conformational transition intermediates of adenylate kinase
-
Feng Y., Yang L., Klockzkowski A., Jernigan R.L. The energy profiles of atomic conformational transition intermediates of adenylate kinase. Proteins 2009, 77:551-558.
-
(2009)
Proteins
, vol.77
, pp. 551-558
-
-
Feng, Y.1
Yang, L.2
Klockzkowski, A.3
Jernigan, R.L.4
-
61
-
-
36749060078
-
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
-
Zhang B.W., Jasnow D., Zuckerman D.M. Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin. Proc Natl Acad Sci USA 2007, 104:18043-18048.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 18043-18048
-
-
Zhang, B.W.1
Jasnow, D.2
Zuckerman, D.M.3
-
62
-
-
44449109605
-
Inherent flexibility and protein function: the open/closed conformational transition in the N-terminal domain of calmodulin
-
Tripathi S., Portman J.J. Inherent flexibility and protein function: the open/closed conformational transition in the N-terminal domain of calmodulin. J Chem Phys 2008, 128:205104.
-
(2008)
J Chem Phys
, vol.128
, pp. 205104
-
-
Tripathi, S.1
Portman, J.J.2
-
63
-
-
36849057606
-
Coarse-grained free energy functions for studying protein conformational changes: a double-well network model
-
Chu J.W., Voth G.A. Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. Biophys J 2007, 93:3860-3871.
-
(2007)
Biophys J
, vol.93
, pp. 3860-3871
-
-
Chu, J.W.1
Voth, G.A.2
-
64
-
-
70349462451
-
Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase
-
Korkut A., Hendrickson W.A. Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. Proc Natl Acad Sci USA 2009, 106:15673-15678.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 15673-15678
-
-
Korkut, A.1
Hendrickson, W.A.2
-
66
-
-
37549009571
-
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding
-
Kim Y.C., Hummer G. Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol 2008, 375:1416-1433.
-
(2008)
J Mol Biol
, vol.375
, pp. 1416-1433
-
-
Kim, Y.C.1
Hummer, G.2
-
68
-
-
70449886281
-
Generalized Yvon-Born-Green theory for molecular systems
-
Mullinax J.W., Noid W.G. Generalized Yvon-Born-Green theory for molecular systems. Phys Rev Lett 2009, 103:198104.
-
(2009)
Phys Rev Lett
, vol.103
, pp. 198104
-
-
Mullinax, J.W.1
Noid, W.G.2
-
69
-
-
61449127303
-
Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120
-
Tan H., Rader A.J. Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120. Proteins 2009, 74:881-894.
-
(2009)
Proteins
, vol.74
, pp. 881-894
-
-
Tan, H.1
Rader, A.J.2
-
70
-
-
40549090981
-
Comparisons of protein family dynamics
-
Rader A.J., Harrell J.T. Comparisons of protein family dynamics. Pac Symp Biocomput 2008, 13:426-437.
-
(2008)
Pac Symp Biocomput
, vol.13
, pp. 426-437
-
-
Rader, A.J.1
Harrell, J.T.2
-
71
-
-
70350714701
-
Comparative analysis of rigidity across protein families
-
Wells S.A., Jimenez-Roldan J.E., Romer R.A. Comparative analysis of rigidity across protein families. Phys Biol 2009, 6:046005.
-
(2009)
Phys Biol
, vol.6
, pp. 046005
-
-
Wells, S.A.1
Jimenez-Roldan, J.E.2
Romer, R.A.3
-
72
-
-
66149154705
-
Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family
-
Mottonen J.M., Xu M., Jacobs D.J., Livesay D.R. Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Proteins 2009, 75:610-627.
-
(2009)
Proteins
, vol.75
, pp. 610-627
-
-
Mottonen, J.M.1
Xu, M.2
Jacobs, D.J.3
Livesay, D.R.4
-
73
-
-
20444429274
-
IGNM: a database of protein functional motions based on Gaussian Network Model
-
Yang L.W., Liu X., Jursa C.J., Holliman M., Rader A.J., Karimi H.A., Bahar I. iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics 2005, 21:2978-2987.
-
(2005)
Bioinformatics
, vol.21
, pp. 2978-2987
-
-
Yang, L.W.1
Liu, X.2
Jursa, C.J.3
Holliman, M.4
Rader, A.J.5
Karimi, H.A.6
Bahar, I.7
-
74
-
-
36549043024
-
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
-
Bahar I., Chennubhotla C., Tobi D. Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 2007, 17:633-640.
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 633-640
-
-
Bahar, I.1
Chennubhotla, C.2
Tobi, D.3
-
75
-
-
61649124866
-
Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle
-
Tehver R., Chen J., Thirumalai D. Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol 2009, 387:390-406.
-
(2009)
J Mol Biol
, vol.387
, pp. 390-406
-
-
Tehver, R.1
Chen, J.2
Thirumalai, D.3
-
76
-
-
70149098505
-
Coarse-grained modeling of allosteric regulation in protein receptors
-
Balabin I.A., Yang W., Beratan D.N. Coarse-grained modeling of allosteric regulation in protein receptors. PNAS 2009, 106:14253-14258.
-
(2009)
PNAS
, vol.106
, pp. 14253-14258
-
-
Balabin, I.A.1
Yang, W.2
Beratan, D.N.3
-
77
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., Pozharski E., Wilson M.A., Petsko G.A., Karplus M., et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 2007, 450:838-844.
-
(2007)
Nature
, vol.450
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
Ott, M.4
Wolf-Watz, M.5
Fenn, T.6
Pozharski, E.7
Wilson, M.A.8
Petsko, G.A.9
Karplus, M.10
-
78
-
-
70350453758
-
Enzyme millisecond conformational dynamics do not catalyze the chemical step
-
Pisliakov A.V., Cao J., Kamerlin S.C., Warshel A. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci USA 2009, 106:17359-17364.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 17359-17364
-
-
Pisliakov, A.V.1
Cao, J.2
Kamerlin, S.C.3
Warshel, A.4
-
79
-
-
77951241004
-
Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models
-
Messer B.M., Roca M., Chu Z.T., Vicatos S., Kilshtain A.V., Warshel A. Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. Proteins 2010, 78:1212-1227.
-
(2010)
Proteins
, vol.78
, pp. 1212-1227
-
-
Messer, B.M.1
Roca, M.2
Chu, Z.T.3
Vicatos, S.4
Kilshtain, A.V.5
Warshel, A.6
-
80
-
-
63449135082
-
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields
-
Whitford P.C., Noel J.K., Gosavi S., Schug A., Sanbonmatsu K.Y., Onuchic J.N. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins 2009, 75:430-441.
-
(2009)
Proteins
, vol.75
, pp. 430-441
-
-
Whitford, P.C.1
Noel, J.K.2
Gosavi, S.3
Schug, A.4
Sanbonmatsu, K.Y.5
Onuchic, J.N.6
-
82
-
-
52649162293
-
Reconstructing atomistic detail for coarse-grained models with resolution exchange
-
Liu P., Shi Q., Lyman E., Voth G.A. Reconstructing atomistic detail for coarse-grained models with resolution exchange. J Chem Phys 2008, 129:114103.
-
(2008)
J Chem Phys
, vol.129
, pp. 114103
-
-
Liu, P.1
Shi, Q.2
Lyman, E.3
Voth, G.A.4
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