-
1
-
-
85061074716
-
Measuring the Conformational Stability of a Protein by Hydrogen Exchange
-
Murphy, K. P. Humana Press Inc: Totowa, NJ
-
Huyghues-Despointes, B. M. P.; Pace, C. N.; Englander, S. W.; Scholtz, J. M. Measuring the Conformational Stability of a Protein by Hydrogen Exchange. In Methods in Molecular Biology; Protein Structure, Stability, and Folding; Murphy, K. P., Ed.; Humana Press Inc: Totowa, NJ, Vol. 168.
-
Methods in Molecular Biology; Protein Structure, Stability, and Folding
, vol.168
-
-
Huyghues-Despointes, B.M.P.1
Pace, C.N.2
Englander, S.W.3
Scholtz, J.M.4
-
2
-
-
0030059689
-
Forces Contributing to the Conformational Stability of Proteins
-
Pace, C. N.; Shirley, B. A.; McNutt, M.; Gajiwala, K. Forces Contributing to the Conformational Stability of Proteins FASEB J. 1996, 10, 75-83
-
(1996)
FASEB J.
, vol.10
, pp. 75-83
-
-
Pace, C.N.1
Shirley, B.A.2
McNutt, M.3
Gajiwala, K.4
-
3
-
-
0025370815
-
Dominant Forces in Protein Folding
-
Dill, K. A. Dominant Forces in Protein Folding Biochemistry 1990, 29, 7133-7155
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
4
-
-
14644435825
-
Intrinsically Unstructured Proteins and Their Functions
-
Dyson, H. J.; Wright, P. E. Intrinsically Unstructured Proteins and Their Functions Nat. Rev. Mol. Cell Biol. 2005, 6, 197-208
-
(2005)
Nat. Rev. Mol. Cell Biol.
, vol.6
, pp. 197-208
-
-
Dyson, H.J.1
Wright, P.E.2
-
5
-
-
0032749078
-
Intrinsically Unstructured Proteins: Re-Assessing the Protein Structure-Function Paradigm
-
Wright, P. E.; Dyson, H. J. Intrinsically Unstructured Proteins: Re-Assessing the Protein Structure-Function Paradigm J. Mol. Biol. 1999, 293, 321-331
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
7
-
-
84903957091
-
Introducing Protein Intrinsic Disorder
-
Habchi, J.; Tompa, P.; Longhi, S.; Uversky, V. N. Introducing Protein Intrinsic Disorder Chem. Rev. 2014, 114, 6561-6588
-
(2014)
Chem. Rev.
, vol.114
, pp. 6561-6588
-
-
Habchi, J.1
Tompa, P.2
Longhi, S.3
Uversky, V.N.4
-
8
-
-
84876281768
-
Unusual Biophysics of Intrinsically Disordered Proteins
-
Uversky, V. N. Unusual Biophysics of Intrinsically Disordered Proteins Biochim. Biophys. Acta, Proteins Proteomics 2013, 1834, 932-951
-
(2013)
Biochim. Biophys. Acta, Proteins Proteomics
, vol.1834
, pp. 932-951
-
-
Uversky, V.N.1
-
9
-
-
84900810032
-
Internal Nanosecond Dynamics in the Intrinsically Disordered Myelin Basic Protein
-
Stadler, A. M.; Stingaciu, L.; Radulescu, A.; Holderer, O.; Monkenbusch, M.; Biehl, R.; Richter, D. Internal Nanosecond Dynamics in the Intrinsically Disordered Myelin Basic Protein J. Am. Chem. Soc. 2014, 136, 6987-6994
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 6987-6994
-
-
Stadler, A.M.1
Stingaciu, L.2
Radulescu, A.3
Holderer, O.4
Monkenbusch, M.5
Biehl, R.6
Richter, D.7
-
10
-
-
84873859687
-
Energetic Basis of Uncoupling Folding from Binding for an Intrinsically Disordered Protein
-
Drobnak, I.; De Jonge, N.; Haesaerts, S.; Vesnaver, G.; Loris, R.; Lah, J. Energetic Basis of Uncoupling Folding from Binding for an Intrinsically Disordered Protein J. Am. Chem. Soc. 2013, 135, 1288-1294
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 1288-1294
-
-
Drobnak, I.1
De Jonge, N.2
Haesaerts, S.3
Vesnaver, G.4
Loris, R.5
Lah, J.6
-
11
-
-
84873828976
-
Folding and Binding of an Intrinsically Disordered Protein: Fast, but Not Diffusion-Limited
-
Rogers, J. M.; Steward, A.; Clarke, J. Folding and Binding of an Intrinsically Disordered Protein: Fast, but Not Diffusion-Limited J. Am. Chem. Soc. 2013, 135, 1415-1422
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 1415-1422
-
-
Rogers, J.M.1
Steward, A.2
Clarke, J.3
-
12
-
-
70350012289
-
Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "fly-Casting" Mechanism
-
Huang, Y. Q.; Liu, Z. R. Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting" Mechanism J. Mol. Biol. 2009, 393, 1143-1159
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 1143-1159
-
-
Huang, Y.Q.1
Liu, Z.R.2
-
13
-
-
69449092251
-
The Importance of Being Flexible: The Case of Basic Region Leucine Zipper Transcriptional Regulators
-
Miller, M. The Importance of Being Flexible: The Case of Basic Region Leucine Zipper Transcriptional Regulators Curr. Protein Pept. Sci. 2009, 10, 244-269
-
(2009)
Curr. Protein Pept. Sci.
, vol.10
, pp. 244-269
-
-
Miller, M.1
-
14
-
-
78649672757
-
Exploring the Trigger Sequence of the GCN4 Coiled-Coil: Biased Molecular Dynamics Resolves Apparent Inconsistencies in NMR Measurements
-
Missimer, J. H.; Dolenc, J.; Steinmetz, M. O.; van Gunsteren, W. F. Exploring the Trigger Sequence of the GCN4 Coiled-Coil: Biased Molecular Dynamics Resolves Apparent Inconsistencies in NMR Measurements Protein Sci. 2010, 19, 2462-2474
-
(2010)
Protein Sci.
, vol.19
, pp. 2462-2474
-
-
Missimer, J.H.1
Dolenc, J.2
Steinmetz, M.O.3
Van Gunsteren, W.F.4
-
15
-
-
34249845041
-
Molecular Basis of Coiled-Coil Formation
-
Steinmetz, M. O.; Jelesarov, I.; Matousek, W. M.; Honnappa, S.; Jahnke, W.; Missimer, J. H.; Frank, S.; Alexandrescu, A. T.; Kammerer, R. A. Molecular Basis of Coiled-Coil Formation Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 7062-7067
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 7062-7067
-
-
Steinmetz, M.O.1
Jelesarov, I.2
Matousek, W.M.3
Honnappa, S.4
Jahnke, W.5
Missimer, J.H.6
Frank, S.7
Alexandrescu, A.T.8
Kammerer, R.A.9
-
16
-
-
33748487166
-
Truncation of a Cross-Linked GCN4-P1 Coiled Coil Leads to Ultrafast Folding
-
Bunagan, M. R.; Cristian, L.; DeGrado, W. F.; Gai, F. Truncation of a Cross-Linked GCN4-P1 Coiled Coil Leads to Ultrafast Folding Biochemistry 2006, 45, 10981-10986
-
(2006)
Biochemistry
, vol.45
, pp. 10981-10986
-
-
Bunagan, M.R.1
Cristian, L.2
Degrado, W.F.3
Gai, F.4
-
17
-
-
0036382925
-
Unfolding of a Leucine Zipper is Not a Simple Two-State Transition
-
Dragan, A. I.; Privalov, P. L. Unfolding of a Leucine Zipper is Not a Simple Two-State Transition J. Mol. Biol. 2002, 321, 891-908
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 891-908
-
-
Dragan, A.I.1
Privalov, P.L.2
-
18
-
-
35349003263
-
Electrostatic Contributions to the Stability of the Gcn4 Leucine Zipper Structure
-
Matousek, W. M.; Ciani, B.; Fitch, C. A.; Garcia-Moreno, B.; Kammerer, R. A.; Alexandrescu, A. T. Electrostatic Contributions to the Stability of the Gcn4 Leucine Zipper Structure J. Mol. Biol. 2007, 374, 206-219
-
(2007)
J. Mol. Biol.
, vol.374
, pp. 206-219
-
-
Matousek, W.M.1
Ciani, B.2
Fitch, C.A.3
Garcia-Moreno, B.4
Kammerer, R.A.5
Alexandrescu, A.T.6
-
19
-
-
8144230244
-
Barrier-Limited, Microsecond Folding of a Stable Protein Measured with Hydrogen Exchange: Implications for Downhill Folding
-
Meisner, W. K.; Sosnick, T. R. Barrier-Limited, Microsecond Folding of a Stable Protein Measured with Hydrogen Exchange: Implications for Downhill Folding Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15639-15644
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 15639-15644
-
-
Meisner, W.K.1
Sosnick, T.R.2
-
20
-
-
4544273743
-
Fast Folding of a Helical Protein Initiated by the Collision of Unstructured Chains
-
Meisner, W. K.; Sosnick, T. R. Fast Folding of a Helical Protein Initiated by the Collision of Unstructured Chains Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 13478-13482
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 13478-13482
-
-
Meisner, W.K.1
Sosnick, T.R.2
-
21
-
-
34249053273
-
NMR Spin State Exchange Spectroscopy Reveals Equilibrium of Two Distinct Conformations of Leucine Zipper GCN4 in Solution
-
Nikolaev, Y.; Pervushin, K. NMR Spin State Exchange Spectroscopy Reveals Equilibrium of Two Distinct Conformations of Leucine Zipper GCN4 in Solution J. Am. Chem. Soc. 2007, 129, 6461-6469
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 6461-6469
-
-
Nikolaev, Y.1
Pervushin, K.2
-
22
-
-
0035252931
-
Coiled Coils: A Highly Versatile Protein Folding Motif
-
Burkhard, P.; Stetefeld, J.; Strelkov, S. V. Coiled Coils: A Highly Versatile Protein Folding Motif Trends Cell Biol. 2001, 11, 82-88
-
(2001)
Trends Cell Biol.
, vol.11
, pp. 82-88
-
-
Burkhard, P.1
Stetefeld, J.2
Strelkov, S.V.3
-
23
-
-
0344628627
-
Historical Review: Another 50th Anniversary: New Periodicities in Coiled Coils
-
Gruber, M.; Lupas, A. N. Historical Review: Another 50th Anniversary: New Periodicities in Coiled Coils Trends Biochem. Sci. 2003, 28, 679-685
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 679-685
-
-
Gruber, M.1
Lupas, A.N.2
-
24
-
-
58149119313
-
A Periodic Table of Coiled-Coil Protein Structures
-
Moutevelis, E.; Woolfson, D. N. A Periodic Table of Coiled-Coil Protein Structures J. Mol. Biol. 2009, 385, 726-732
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 726-732
-
-
Moutevelis, E.1
Woolfson, D.N.2
-
25
-
-
84946455932
-
Entropy Estimation from Simulations of Non-Diffusive Systems
-
Edholm, O.; Berendsen, H. J. C. Entropy Estimation from Simulations of Non-Diffusive Systems Mol. Phys. 1984, 51, 1011-1028
-
(1984)
Mol. Phys.
, vol.51
, pp. 1011-1028
-
-
Edholm, O.1
Berendsen, H.J.C.2
-
26
-
-
18344362394
-
Use of Classical Statistical-Mechanics in Treatment of Polymer-Chain Conformation
-
Go, N.; Scheraga, H. A. Use of Classical Statistical-Mechanics in Treatment of Polymer-Chain Conformation Macromolecules 1976, 9, 535-542
-
(1976)
Macromolecules
, vol.9
, pp. 535-542
-
-
Go, N.1
Scheraga, H.A.2
-
27
-
-
51149216498
-
Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules
-
Go, N.; Scheraga, H. A. Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules J. Chem. Phys. 1969, 51, 4751-4767
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 4751-4767
-
-
Go, N.1
Scheraga, H.A.2
-
28
-
-
34247339716
-
Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States
-
Noe, F.; Horenko, I.; Schutte, C.; Smith, J. C. 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
-
-
Noe, F.1
Horenko, I.2
Schutte, C.3
Smith, J.C.4
-
29
-
-
79959761281
-
Which Similarity Measure Is Better for Analyzing Protein Structures in a Molecular Dynamics Trajectory?
-
Cossio, P.; Laio, A.; Pietrucci, F. Which Similarity Measure Is Better for Analyzing Protein Structures in a Molecular Dynamics Trajectory? Phys. Chem. Chem. Phys. 2011, 13, 10421-10425
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 10421-10425
-
-
Cossio, P.1
Laio, A.2
Pietrucci, F.3
-
30
-
-
84865064420
-
Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric
-
Zhou, T.; Caflisch, A. Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric J. Chem. Theory Comp. 2012, 8, 2930-2937
-
(2012)
J. Chem. Theory Comp.
, vol.8
, pp. 2930-2937
-
-
Zhou, T.1
Caflisch, A.2
-
32
-
-
84902664221
-
Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins
-
Echeverria, I.; Makarov, D. E.; Papoian, G. A. Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins J. Am. Chem. Soc. 2014, 136, 8708-8713
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 8708-8713
-
-
Echeverria, I.1
Makarov, D.E.2
Papoian, G.A.3
-
33
-
-
33846398927
-
Polypeptide Motions Are Dominated by Peptide Group Oscillations Resulting from Dihedral Angle Correlations between Nearest Neighbors
-
Fitzgerald, J. E.; Jha, A. K.; Sosnick, T. R.; Freed, K. F. Polypeptide Motions Are Dominated by Peptide Group Oscillations Resulting from Dihedral Angle Correlations between Nearest Neighbors† Biochemistry 2006, 46, 669-682
-
(2006)
Biochemistry
, vol.46
, pp. 669-682
-
-
Fitzgerald, J.E.1
Jha, A.K.2
Sosnick, T.R.3
Freed, K.F.4
-
34
-
-
0000521185
-
Theory of the Kinetics of Conformational Transitions in Polymers
-
Helfand, E. Theory of the Kinetics of Conformational Transitions in Polymers J. Chem. Phys. 1971, 54, 4651-4661
-
(1971)
J. Chem. Phys.
, vol.54
, pp. 4651-4661
-
-
Helfand, E.1
-
35
-
-
63749108613
-
In Silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides
-
Li, D. W.; Bruschweiler, R. In Silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides. Phys. Rev. Lett. 2009, 102.
-
(2009)
Phys. Rev. Lett.
, vol.102
-
-
Li, D.W.1
Bruschweiler, R.2
-
36
-
-
0039563769
-
Collective Motions of Myosin Head Derived from Backbone Molecular Dynamics and Combination with X-Ray Solution Scattering Data
-
Higo, J.; Sugimoto, Y.; Wakabayashi, K.; Nakamura, H. Collective Motions of Myosin Head Derived from Backbone Molecular Dynamics and Combination with X-Ray Solution Scattering Data J. Comput. Chem. 2001, 22, 1983-1994
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1983-1994
-
-
Higo, J.1
Sugimoto, Y.2
Wakabayashi, K.3
Nakamura, H.4
-
37
-
-
33847642496
-
Nearest-Neighbor Nonparametric Method for Estimating the Configurational Entropy of Complex Molecules
-
Hnizdo, V.; Darian, E.; Fedorowicz, A.; Demchuk, E.; Li, S.; Singh, H. Nearest-Neighbor Nonparametric Method for Estimating the Configurational Entropy of Complex Molecules J. Comput. Chem. 2007, 28, 655-668
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 655-668
-
-
Hnizdo, V.1
Darian, E.2
Fedorowicz, A.3
Demchuk, E.4
Li, S.5
Singh, H.6
-
38
-
-
0000127140
-
Method for Estimating the Configurational Entropy of Macromolecules
-
Karplus, M.; Kushick, J. N. Method for Estimating the Configurational Entropy of Macromolecules Macromolecules 1981, 14, 325-332
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.N.2
-
39
-
-
48549083172
-
Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation
-
Miyano, S. DeLisi, C. Holzhutter, H. G. Kanehisa, M. Vol
-
Numata, J.; Wan, M.; Knapp, E. W. Conformational Entropy of Biomolecules: Beyond the Quasi-Harmonic Approximation. In Genome Informatics 2007; Miyano, S.; DeLisi, C.; Holzhutter, H. G.; Kanehisa, M., Eds.; 2007; Vol. 18, pp 192-205.
-
(2007)
Genome Informatics 2007
, vol.18
, pp. 192-205
-
-
Numata, J.1
Wan, M.2
Knapp, E.W.3
-
40
-
-
0001351515
-
Estimation of Absolute and Relative Entropies of Macromolecules Using the Covariance-Matrix
-
Schlitter, J. Estimation of Absolute and Relative Entropies of Macromolecules Using the Covariance-Matrix Chem. Phys. Lett. 1993, 215, 617-621
-
(1993)
Chem. Phys. Lett.
, vol.215
, pp. 617-621
-
-
Schlitter, J.1
-
43
-
-
84862221556
-
Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion
-
McClendon, C. L.; Hua, L.; Barreiro, G.; Jacobson, M. P. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion J. Chem. Theory Comp. 2012, 8, 2115-2126
-
(2012)
J. Chem. Theory Comp.
, vol.8
, pp. 2115-2126
-
-
McClendon, C.L.1
Hua, L.2
Barreiro, G.3
Jacobson, M.P.4
-
44
-
-
65449130754
-
Mist: Maximum Information Spanning Trees for Dimension Reduction of Biological Data Sets
-
King, B. M.; Tidor, B. Mist: Maximum Information Spanning Trees for Dimension Reduction of Biological Data Sets Bioinformatics 2009, 25, 1165-1172
-
(2009)
Bioinformatics
, vol.25
, pp. 1165-1172
-
-
King, B.M.1
Tidor, B.2
-
45
-
-
84858068315
-
Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation
-
King, B. M.; Silver, N. W.; Tidor, B. Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation J. Phys. Chem. B 2012, 116, 2891-2904
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 2891-2904
-
-
King, B.M.1
Silver, N.W.2
Tidor, B.3
-
46
-
-
84885611062
-
Microscopic Insights into the NMR Relaxation-Based Protein Conformational Entropy Meter
-
Kasinath, V.; Sharp, K. A.; Wand, A. J. Microscopic Insights into the NMR Relaxation-Based Protein Conformational Entropy Meter J. Am. Chem. Soc. 2013, 135, 15092-15100
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 15092-15100
-
-
Kasinath, V.1
Sharp, K.A.2
Wand, A.J.3
-
47
-
-
0037457815
-
Dynamics and Entropy of a Calmodulin-Peptide Complex Studied by NMR and Molecular Dynamics
-
Prabhu, N. V.; Lee, A. L.; Wand, A. J.; Sharp, K. A. Dynamics and Entropy of a Calmodulin-Peptide Complex Studied by NMR and Molecular Dynamics Biochemistry 2003, 42, 562-570
-
(2003)
Biochemistry
, vol.42
, pp. 562-570
-
-
Prabhu, N.V.1
Lee, A.L.2
Wand, A.J.3
Sharp, K.A.4
-
48
-
-
84870579518
-
Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding
-
Fenley, A. T.; Muddana, H. S.; Gilson, M. K. Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 20006-20011
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 20006-20011
-
-
Fenley, A.T.1
Muddana, H.S.2
Gilson, M.K.3
-
49
-
-
84902971173
-
Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems
-
Fenley, A. T.; Killian, B. J.; Hnizdo, V.; Fedorowicz, A.; Sharp, D. S.; Gilson, M. K. Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems J. Phys. Chem. B 2014, 118, 6447-6455
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 6447-6455
-
-
Fenley, A.T.1
Killian, B.J.2
Hnizdo, V.3
Fedorowicz, A.4
Sharp, D.S.5
Gilson, M.K.6
-
50
-
-
34547227692
-
Extraction of Configurational Entropy from Molecular Simulations Via an Expansion Approximation
-
Killian, B. J.; Yundenfreund Kravitz, J.; Gilson, M. K. Extraction of Configurational Entropy from Molecular Simulations Via an Expansion Approximation J. Chem. Phys. 2007, 127, 024107
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 024107
-
-
Killian, B.J.1
Yundenfreund Kravitz, J.2
Gilson, M.K.3
-
51
-
-
73349111643
-
Quantifying Correlations between Allosteric Sites in Thermodynamic Ensembles
-
McClendon, C. L.; Friedland, G.; Mobley, D. L.; Amirkhani, H.; Jacobson, M. P. Quantifying Correlations between Allosteric Sites in Thermodynamic Ensembles J. Chem. Theory Comp. 2009, 5, 2486-2502
-
(2009)
J. Chem. Theory Comp.
, vol.5
, pp. 2486-2502
-
-
McClendon, C.L.1
Friedland, G.2
Mobley, D.L.3
Amirkhani, H.4
Jacobson, M.P.5
-
52
-
-
65549109031
-
Configurational Entropy in Protein-Peptide Binding: Computational Study of Tsg101 Ubiquitin E2 Variant Domain with an Hiv-Derived Ptap Nonapeptide
-
Killian, B. J.; Kravitz, J. Y.; Somani, S.; Dasgupta, P.; Pang, Y.-P.; Gilson, M. K. Configurational Entropy in Protein-Peptide Binding: Computational Study of Tsg101 Ubiquitin E2 Variant Domain with an Hiv-Derived Ptap Nonapeptide J. Mol. Biol. 2009, 389, 315-335
-
(2009)
J. Mol. Biol.
, vol.389
, pp. 315-335
-
-
Killian, B.J.1
Kravitz, J.Y.2
Somani, S.3
Dasgupta, P.4
Pang, Y.-P.5
Gilson, M.K.6
-
53
-
-
84865736993
-
Multibody Local Approximation: Application to Conformational Entropy Calculations on Biomolecules
-
Suarez, E.; Suarez, D. Multibody Local Approximation: Application to Conformational Entropy Calculations on Biomolecules J. Chem. Phys. 2012, 137, 084115
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 084115
-
-
Suarez, E.1
Suarez, D.2
-
54
-
-
84880697996
-
Cencalc: A Computational Tool for Conformational Entropy Calculations from Molecular Simulations
-
Suarez, E.; Diaz, N.; Mendez, J.; Suarez, D. Cencalc: A Computational Tool for Conformational Entropy Calculations from Molecular Simulations J. Comput. Chem. 2013, 34, 2041-2054
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2041-2054
-
-
Suarez, E.1
Diaz, N.2
Mendez, J.3
Suarez, D.4
-
55
-
-
84907992130
-
Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations
-
Suarez, D.; Diaz, N. Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations J. Chem. Theory Comput. 2014, 10, 4718-4729
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 4718-4729
-
-
Suarez, D.1
Diaz, N.2
-
57
-
-
80053979296
-
Msmbuilder2: Modeling Conformational Dynamics on 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 on the Picosecond to Millisecond Scale J. Chem. Theory Comput. 2011, 7, 3412-3419
-
(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
-
58
-
-
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
-
(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
-
59
-
-
84874919177
-
Atomistic Simulations of Wimley-White Pentapeptides: Sampling of Structure and Dynamics in Solution
-
Singh, G.; Tieleman, D. P. Atomistic Simulations of Wimley-White Pentapeptides: Sampling of Structure and Dynamics in Solution J. Chem. Theory Comput. 2013, 9, 1657-1666
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 1657-1666
-
-
Singh, G.1
Tieleman, D.P.2
-
60
-
-
36649006642
-
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
-
Shao, J. Y.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2312-2334
-
-
Shao, J.Y.1
Tanner, S.W.2
Thompson, N.3
Cheatham, T.E.4
-
62
-
-
79951969616
-
Efficient Quantification of the Importance of Contacts for the Dynamical Stability of Proteins
-
Hamacher, K. Efficient Quantification of the Importance of Contacts for the Dynamical Stability of Proteins J. Comput. Chem. 2011, 32, 810-815
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 810-815
-
-
Hamacher, K.1
-
63
-
-
84862221556
-
Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion
-
McClendon, C. L.; Hua, L.; Barreiro, G.; Jacobson, M. P. Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion J. Chem. Theory Comput. 2012, 8, 2115-2126
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2115-2126
-
-
McClendon, C.L.1
Hua, L.2
Barreiro, G.3
Jacobson, M.P.4
-
64
-
-
84861120582
-
Quantitative Comparison of Conformational Ensembles
-
Wolfe, K. C.; Chirikjian, G. S. Quantitative Comparison of Conformational Ensembles Entropy 2012, 14, 213-232
-
(2012)
Entropy
, vol.14
, pp. 213-232
-
-
Wolfe, K.C.1
Chirikjian, G.S.2
-
65
-
-
0003544049
-
-
Vdf hochschulverlag AG an der ETH: Zürich
-
van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P. Biomolecular Simulation: The Gromos96 Manual and User Guide. Vdf hochschulverlag AG an der ETH: Zürich, 1996.
-
(1996)
Biomolecular Simulation: The Gromos96 Manual and User Guide
-
-
Van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.R.P.7
-
66
-
-
67650299002
-
Hamiltonian Replica Exchange Method Studies of a Leucine Zipper Dimer
-
Su, L.; Cukier, R. I. Hamiltonian Replica Exchange Method Studies of a Leucine Zipper Dimer J. Phys. Chem. B 2009, 113, 9595-9605
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9595-9605
-
-
Su, L.1
Cukier, R.I.2
-
67
-
-
0026331267
-
X-Ray Structure of the GCN4 Leucine Zipper, a 2-Stranded, Parallel Coiled Coil
-
OShea, E. K.; Klemm, J. D.; Kim, P. S.; Alber, T. X-Ray Structure of the GCN4 Leucine Zipper, a 2-Stranded, Parallel Coiled Coil Science 1991, 254, 539-544
-
(1991)
Science
, vol.254
, pp. 539-544
-
-
Oshea, E.K.1
Klemm, J.D.2
Kim, P.S.3
Alber, T.4
-
68
-
-
84929343121
-
-
Michigan State University: East Lansing
-
Lou, H.; Cukier, R. I. Analyzer, 2.0; Michigan State University: East Lansing, 2008.
-
(2008)
Analyzer, 2.0
-
-
Lou, H.1
Cukier, R.I.2
-
70
-
-
0034825161
-
A Strategy for Analysis of (Molecular) Equilibrium Simulations: Configuration Space Density Estimation, Clustering, and Visualization
-
Hamprecht, F. A.; Peter, C.; Daura, X.; Thiel, W.; van Gunsteren, W. F. A Strategy for Analysis of (Molecular) Equilibrium Simulations: Configuration Space Density Estimation, Clustering, and Visualization J. Chem. Phys. 2001, 114, 2079-2089
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 2079-2089
-
-
Hamprecht, F.A.1
Peter, C.2
Daura, X.3
Thiel, W.4
Van Gunsteren, W.F.5
-
71
-
-
0023475026
-
Configurational Entropy of Native Proteins
-
Karplus, M.; Ichiye, T.; Pettitt, B. M. Configurational Entropy of Native Proteins Biophys. J. 1987, 52, 1083-1085
-
(1987)
Biophys. J.
, vol.52
, pp. 1083-1085
-
-
Karplus, M.1
Ichiye, T.2
Pettitt, B.M.3
-
72
-
-
33846822002
-
Ligand Configurational Entropy and Protein Binding
-
Chang, C.-e. A.; Chen, W.; Gilson, M. K. Ligand Configurational Entropy and Protein Binding Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1534-1539
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 1534-1539
-
-
Chang, C.-E.A.1
Chen, W.2
Gilson, M.K.3
|