메뉴 건너뛰기




Volumn 119, Issue 9, 2015, Pages 3621-3634

Dihedral angle entropy measures for intrinsically disordered proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; CONFORMATIONS; DIMERS; DISTRIBUTION FUNCTIONS; ENTROPY; FREE ENERGY; MOLECULAR DYNAMICS; PROBABILITY DISTRIBUTIONS; PROTEINS;

EID: 84929327450     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp5102412     Document Type: Article
Times cited : (17)

References (72)
  • 2
    • 0030059689 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 8
    • 84876281768 scopus 로고    scopus 로고
    • 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
  • 10
    • 84873859687 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 16
    • 33748487166 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 19
    • 8144230244 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 52
    • 65549109031 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 59
    • 84874919177 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 66
    • 67650299002 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 69
  • 70
    • 0034825161 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.