-
1
-
-
0037093869
-
Electron Spin Resonance in Studies of Membranes and Proteins
-
Borbat, P. P.; Mchaourab, H. S.; Freed, J. H. Electron Spin Resonance in Studies of Membranes and Proteins J. Am. Chem. Soc. 2002, 124, 5304-5314
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5304-5314
-
-
Borbat, P.P.1
McHaourab, H.S.2
Freed, J.H.3
-
2
-
-
34250874047
-
Rigid Body Refinement of Protein Complexes with Long-Range Distance Restraints from Pulsed Dipolar ESR
-
Bhatnagar, J.; Freed, J. H.; Crane, B. R. Rigid Body Refinement of Protein Complexes with Long-Range Distance Restraints from Pulsed Dipolar ESR Methods Enzymol. 2007, 423, 117-133
-
(2007)
Methods Enzymol.
, vol.423
, pp. 117-133
-
-
Bhatnagar, J.1
Freed, J.H.2
Crane, B.R.3
-
3
-
-
79851516036
-
Algorithm for Selection of Optimized EPR Distance Restraints for de Novo Protein Structure Determination
-
Kazmier, K.; Alexander, N. S.; Meiler, J.; Mchaourab, H. S. Algorithm for Selection of Optimized EPR Distance Restraints for De Novo Protein Structure Determination J. Struct. Biol. 2011, 173, 549-557
-
(2011)
J. Struct. Biol.
, vol.173
, pp. 549-557
-
-
Kazmier, K.1
Alexander, N.S.2
Meiler, J.3
McHaourab, H.S.4
-
4
-
-
0035799354
-
Molecular Motion of Spin Labeled Side Chains in Alpha-Helices: Analysis by Variation of Side Chain Structure
-
Columbus, L.; Kalai, T.; Jeko, J.; Hideg, K.; Hubbell, W. L. Molecular Motion of Spin Labeled Side Chains in Alpha-Helices: Analysis by Variation of Side Chain Structure Biochemistry 2001, 40, 3828-3846
-
(2001)
Biochemistry
, vol.40
, pp. 3828-3846
-
-
Columbus, L.1
Kalai, T.2
Jeko, J.3
Hideg, K.4
Hubbell, W.L.5
-
5
-
-
0000690883
-
Ab Initio Molecular Orbital Studies of the Rotational Barriers and the S-33 and C-13 Chemical Shieldings for Dimethyl Disulfide
-
Jiao, D.; Barfield, M.; Combariza, J. E.; Hruby, V. J. Ab Initio Molecular Orbital Studies of the Rotational Barriers and the S-33 and C-13 Chemical Shieldings for Dimethyl Disulfide J. Am. Chem. Soc. 1992, 114, 3639-3643
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 3639-3643
-
-
Jiao, D.1
Barfield, M.2
Combariza, J.E.3
Hruby, V.J.4
-
6
-
-
0029905422
-
Motion of Spin-Labeled Side Chains in T4 Lysozyme, Correlation with Protein Structure and Dynamics
-
Mchaourab, H. S.; Lietzow, M. A.; Hideg, K.; Hubbell, W. L. Motion of Spin-Labeled Side Chains in T4 Lysozyme, Correlation with Protein Structure and Dynamics Biochemistry 1996, 35, 7692-7704
-
(1996)
Biochemistry
, vol.35
, pp. 7692-7704
-
-
McHaourab, H.S.1
Lietzow, M.A.2
Hideg, K.3
Hubbell, W.L.4
-
8
-
-
0033000691
-
A Multifrequency Electron Spin Resonance Study of T4 Lysozyme Dynamics
-
Barnes, J. P.; Liang, Z. C.; Mchaourab, H. S.; Freed, J. H.; Hubbell, W. L. A Multifrequency Electron Spin Resonance Study of T4 Lysozyme Dynamics Biophys. J. 1999, 76, 3298-3306
-
(1999)
Biophys. J.
, vol.76
, pp. 3298-3306
-
-
Barnes, J.P.1
Liang, Z.C.2
McHaourab, H.S.3
Freed, J.H.4
Hubbell, W.L.5
-
9
-
-
38649125853
-
Structural Determinants of Nitroxide Motion in Spin-Labeled Proteins: Solvent-Exposed Sites in Helix B of T4 Lysozyme
-
Guo, Z. F.; Cascio, D.; Hideg, K.; Hubbell, W. L. Structural Determinants of Nitroxide Motion in Spin-Labeled Proteins: Solvent-Exposed Sites in Helix B of T4 Lysozyme Protein Sci. 2008, 17, 228-239
-
(2008)
Protein Sci.
, vol.17
, pp. 228-239
-
-
Guo, Z.F.1
Cascio, D.2
Hideg, K.3
Hubbell, W.L.4
-
10
-
-
34249794011
-
Structural Determinants of Nitroxide Motion in Spin-Labeled Proteins: Tertiary Contact and Solvent-Inaccessible Sites in Helix G of T4 Lysozyme
-
Guo, Z. F.; Cascio, D.; Hideg, K.; Kalai, T.; Hubbell, W. L. Structural Determinants of Nitroxide Motion in Spin-Labeled Proteins: Tertiary Contact and Solvent-Inaccessible Sites in Helix G of T4 Lysozyme Protein Sci. 2007, 16, 1069-1086
-
(2007)
Protein Sci.
, vol.16
, pp. 1069-1086
-
-
Guo, Z.F.1
Cascio, D.2
Hideg, K.3
Kalai, T.4
Hubbell, W.L.5
-
11
-
-
80053650255
-
Structure and Dynamics of a Conformationally Constrained Nitroxide Side Chain and Applications in EPR Apectroscopy
-
Fleissner, M. R.; Bridges, M. D.; Brooks, E. K.; Cascio, D.; Kalai, T.; Hideg, K.; Hubbell, W. L. Structure and Dynamics of a Conformationally Constrained Nitroxide Side Chain and Applications in EPR Apectroscopy Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16241-16246
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 16241-16246
-
-
Fleissner, M.R.1
Bridges, M.D.2
Brooks, E.K.3
Cascio, D.4
Kalai, T.5
Hideg, K.6
Hubbell, W.L.7
-
12
-
-
65649117362
-
Structural Origin of Weakly Ordered Nitroxide Motion in Spin-Labeled Proteins
-
Fleissner, M. R.; Cascio, D.; Hubbell, W. L. Structural Origin of Weakly Ordered Nitroxide Motion in Spin-Labeled Proteins Protein Sci. 2009, 18, 893-908
-
(2009)
Protein Sci.
, vol.18
, pp. 893-908
-
-
Fleissner, M.R.1
Cascio, D.2
Hubbell, W.L.3
-
13
-
-
84877046509
-
-
Ph.D. Thesis, University of California, Los Angeles.
-
Fleissner, M. R. Ph.D. Thesis, University of California, Los Angeles, 2007.
-
(2007)
-
-
Fleissner, M.R.1
-
15
-
-
0039171268
-
Crystal Structures of Spin Labeled T4 Lysozyme Mutants: Implications for the Interpretation of EPR Spectra in Terms of Structure
-
Langen, R.; Oh, K. J.; Cascio, D.; Hubbell, W. L. Crystal Structures of Spin Labeled T4 Lysozyme Mutants: Implications for the Interpretation of EPR Spectra in Terms of Structure Biochemistry 2000, 39, 8396-8406
-
(2000)
Biochemistry
, vol.39
, pp. 8396-8406
-
-
Langen, R.1
Oh, K.J.2
Cascio, D.3
Hubbell, W.L.4
-
16
-
-
33846352840
-
Dynamics of the Nitroxide Side Chain in Spin-Labeled Proteins
-
Tombolato, F.; Ferrarini, A.; Freed, J. H. Dynamics of the Nitroxide Side Chain in Spin-Labeled Proteins J. Phys. Chem. B 2006, 110, 26248-26259
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 26248-26259
-
-
Tombolato, F.1
Ferrarini, A.2
Freed, J.H.3
-
17
-
-
33846365968
-
Modeling the Effects of Structure and Dynamics of the Nitroxide Side Chain on the ESR Spectra of Spin-Labeled Proteins
-
Tombolato, F.; Ferrarini, A.; Freed, J. H. Modeling the Effects of Structure and Dynamics of the Nitroxide Side Chain on the ESR Spectra of Spin-Labeled Proteins J. Phys. Chem. B 2006, 110, 26260-26271
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 26260-26271
-
-
Tombolato, F.1
Ferrarini, A.2
Freed, J.H.3
-
18
-
-
78651466789
-
Conformational Analysis of a Nitroxide Side Chain in an Alpha-Helix with Density Functional Theory
-
Warshaviak, D. T.; Serbulea, L.; Houk, K. N.; Hubbell, W. L. Conformational Analysis of a Nitroxide Side Chain in an Alpha-Helix with Density Functional Theory J. Phys. Chem. B 2011, 115, 397-405
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 397-405
-
-
Warshaviak, D.T.1
Serbulea, L.2
Houk, K.N.3
Hubbell, W.L.4
-
19
-
-
43949138917
-
Parametrization, Molecular Dynamics Simulation, and Calculation of Electron Spin Resonance Spectra of a Nitroxide Spin Label on a Polyalanine Alpha-Helix
-
Sezer, D.; Freed, J. H.; Roux, B. Parametrization, Molecular Dynamics Simulation, and Calculation of Electron Spin Resonance Spectra of a Nitroxide Spin Label on a Polyalanine Alpha-Helix J. Phys. Chem. B 2008, 112, 5755-5767
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 5755-5767
-
-
Sezer, D.1
Freed, J.H.2
Roux, B.3
-
20
-
-
52349122099
-
Using Markov Models to Simulate Electron Spin Resonance Spectra from Molecular Dynamics Trajectories
-
Sezer, D.; Freed, J. H.; Roux, B. Using Markov Models to Simulate Electron Spin Resonance Spectra from Molecular Dynamics Trajectories J. Phys. Chem. B 2008, 112, 11014-11027
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 11014-11027
-
-
Sezer, D.1
Freed, J.H.2
Roux, B.3
-
21
-
-
67749091066
-
Multifrequency Electron Spin Resonance Spectra of a Spin-Labeled Protein Calculated from Molecular Dynamics Simulations
-
Sezer, D.; Freed, J. H.; Roux, B. Multifrequency Electron Spin Resonance Spectra of a Spin-Labeled Protein Calculated from Molecular Dynamics Simulations J. Am. Chem. Soc. 2009, 131, 2597-2605
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 2597-2605
-
-
Sezer, D.1
Freed, J.H.2
Roux, B.3
-
22
-
-
33947620119
-
Spin Pair Geometry Revealed by High-Field DEER in the Presence of Conformational Distributions
-
Polyhach, Y.; Godt, A.; Bauer, C.; Jeschke, G. Spin Pair Geometry Revealed by High-Field DEER in the Presence of Conformational Distributions J. Magn. Reson. 2007, 185, 118-129
-
(2007)
J. Magn. Reson.
, vol.185
, pp. 118-129
-
-
Polyhach, Y.1
Godt, A.2
Bauer, C.3
Jeschke, G.4
-
23
-
-
48749113684
-
Atomistic Insights into Rhodopsin Activation from a Dynamic Model
-
Tikhonova, I. G.; Best, R. B.; Engel, S.; Gershengorn, M. C.; Hummer, G.; Costanzi, S. Atomistic Insights into Rhodopsin Activation from a Dynamic Model J. Am. Chem. Soc. 2008, 130, 10141-10149
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 10141-10149
-
-
Tikhonova, I.G.1
Best, R.B.2
Engel, S.3
Gershengorn, M.C.4
Hummer, G.5
Costanzi, S.6
-
24
-
-
44949121782
-
Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments
-
Ding, F.; Layten, M.; Simmerling, C. Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments J. Am. Chem. Soc. 2008, 130, 7184-7185
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 7184-7185
-
-
Ding, F.1
Layten, M.2
Simmerling, C.3
-
25
-
-
21644446664
-
Explicit Treatment of Spin Labels in Modeling of Distance Constraints from Dipolar EPR and DEER
-
Sale, K.; Song, L. K.; Liu, Y. S.; Perozo, E.; Fajer, P. Explicit Treatment of Spin Labels in Modeling of Distance Constraints from Dipolar EPR and DEER J. Am. Chem. Soc. 2005, 127, 9334-9335
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 9334-9335
-
-
Sale, K.1
Song, L.K.2
Liu, Y.S.3
Perozo, E.4
Fajer, P.5
-
26
-
-
79959371395
-
Solution Structure of the ESCRT-I Complex by Small-Angle X-ray Scattering, EPR, and FRET Spectroscopy
-
Boura, E.; Rozycki, B.; Herrick, D. Z.; Chung, H. S.; Vecer, J.; Eaton, W. A.; Cafiso, D. S.; Hummer, G.; Hurley, J. H. Solution Structure of the ESCRT-I Complex by Small-Angle X-ray Scattering, EPR, and FRET Spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 9437-9442
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 9437-9442
-
-
Boura, E.1
Rozycki, B.2
Herrick, D.Z.3
Chung, H.S.4
Vecer, J.5
Eaton, W.A.6
Cafiso, D.S.7
Hummer, G.8
Hurley, J.H.9
-
27
-
-
79851512251
-
RosettaEPR: An Integrated Tool for Protein Structure Determination from Sparse EPR Data
-
Hirst, S. J.; Alexander, N.; Mchaourab, H. S.; Meiler, J. RosettaEPR: An Integrated Tool for Protein Structure Determination from Sparse EPR Data J. Struct. Biol. 2011, 173, 506-514
-
(2011)
J. Struct. Biol.
, vol.173
, pp. 506-514
-
-
Hirst, S.J.1
Alexander, N.2
McHaourab, H.S.3
Meiler, J.4
-
28
-
-
79251562868
-
Rotamer Libraries of Spin Labelled Cysteines for Protein Studies
-
Polyhach, Y.; Bordignon, E.; Jeschke, G. Rotamer Libraries of Spin Labelled Cysteines for Protein Studies Phys. Chem. Chem. Phys. 2011, 13, 2356-2366
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 2356-2366
-
-
Polyhach, Y.1
Bordignon, E.2
Jeschke, G.3
-
29
-
-
84859888767
-
DEER Distance Measurements on Proteins
-
Jeschke, G. DEER Distance Measurements on Proteins Annu. Rev. Phys. Chem. 2012, 63, 419-446
-
(2012)
Annu. Rev. Phys. Chem.
, vol.63
, pp. 419-446
-
-
Jeschke, G.1
-
30
-
-
80055041655
-
Computer Modeling of Nitroxide Spin Labels on Proteins
-
Hatmal, M. M.; Li, Y.; Hegde, B. G.; Hegde, P. B.; Jao, C. C.; Langen, R.; Haworth, I. S. Computer Modeling of Nitroxide Spin Labels on Proteins Biopolymers 2012, 97, 35-44
-
(2012)
Biopolymers
, vol.97
, pp. 35-44
-
-
Hatmal, M.M.1
Li, Y.2
Hegde, B.G.3
Hegde, P.B.4
Jao, C.C.5
Langen, R.6
Haworth, I.S.7
-
31
-
-
3543012707
-
Crystallography & NMR system: A New Software Suite for Macromolecular Structure Determination
-
Brunger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Crystallography & NMR system: A New Software Suite for Macromolecular Structure Determination Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 905-921
-
(1998)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
32
-
-
12944304172
-
Mapping Long-Range Interactions in Alpha-Synuclein Using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
-
Dedmon, M. M.; Lindorff-Larsen, K.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. Mapping Long-Range Interactions in Alpha-Synuclein Using Spin-Label NMR and Ensemble Molecular Dynamics Simulations J. Am. Chem. Soc. 2005, 127, 476-477
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 476-477
-
-
Dedmon, M.M.1
Lindorff-Larsen, K.2
Christodoulou, J.3
Vendruscolo, M.4
Dobson, C.M.5
-
33
-
-
12744263121
-
Simultaneous Determination of Protein Structure and Dynamics
-
Lindorff-Larsen, K.; Best, R. B.; DePristo, M. A.; Dobson, C. M.; Vendruscolo, M. Simultaneous Determination of Protein Structure and Dynamics Nature 2005, 433, 128-132
-
(2005)
Nature
, vol.433
, pp. 128-132
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Depristo, M.A.3
Dobson, C.M.4
Vendruscolo, M.5
-
34
-
-
27244432202
-
Interpreting Dynamically-Averaged Scalar Couplings in Proteins
-
Lindorff-Larsen, K.; Best, R. B.; Vendruscolo, M. Interpreting Dynamically-Averaged Scalar Couplings in Proteins J. Biomol. NMR 2005, 32, 273-280
-
(2005)
J. Biomol. NMR
, vol.32
, pp. 273-280
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Vendruscolo, M.3
-
35
-
-
33746652529
-
Relation between Native Ensembles and Experimental Structures of Proteins
-
Best, R. B.; Lindorff-Larsen, K.; DePristo, M. A.; Vendruscolo, M. Relation Between Native Ensembles and Experimental Structures of Proteins Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 10901-10906
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 10901-10906
-
-
Best, R.B.1
Lindorff-Larsen, K.2
Depristo, M.A.3
Vendruscolo, M.4
-
36
-
-
11844289547
-
Protein Folding and the Organization of the Protein Topology Universe
-
Lindorff-Larsen, K.; Rogen, P.; Paci, E.; Vendruscolo, M.; Dobson, C. M. Protein Folding and the Organization of the Protein Topology Universe Trends. Biochem. Sci. 2005, 30, 13-19
-
(2005)
Trends. Biochem. Sci.
, vol.30
, pp. 13-19
-
-
Lindorff-Larsen, K.1
Rogen, P.2
Paci, E.3
Vendruscolo, M.4
Dobson, C.M.5
-
37
-
-
44649087026
-
Application of Solid-State NMR Restraint Potentials in Membrane Protein Modeling
-
Lee, J.; Chen, J. H.; Brooks, C. L.; Im, W. P. Application of Solid-State NMR Restraint Potentials in Membrane Protein Modeling J. Magn. Reson. 2008, 193, 68-76
-
(2008)
J. Magn. Reson.
, vol.193
, pp. 68-76
-
-
Lee, J.1
Chen, J.H.2
Brooks, C.L.3
Im, W.P.4
-
38
-
-
79960326994
-
Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables
-
Jo, S.; Im, W. Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables Biophys. J. 2011, 100, 2913-2921
-
(2011)
Biophys. J.
, vol.100
, pp. 2913-2921
-
-
Jo, S.1
Im, W.2
-
39
-
-
79960322991
-
Solid-State NMR Ensemble Dynamics as a Mediator between Experiment and Simulation
-
Kim, T.; Jo, S.; Im, W. Solid-State NMR Ensemble Dynamics as a Mediator Between Experiment and Simulation Biophys. J. 2011, 100, 2922-2928
-
(2011)
Biophys. J.
, vol.100
, pp. 2922-2928
-
-
Kim, T.1
Jo, S.2
Im, W.3
-
40
-
-
84855469558
-
An Ensemble Dynamics Approach to Decipher Solid-State NMR Observables of Membrane Proteins
-
Im, W.; Jo, S.; Kim, T. An Ensemble Dynamics Approach to Decipher Solid-State NMR Observables of Membrane Proteins Biochim. Biophys. Acta 2012, 1818, 252-262
-
(2012)
Biochim. Biophys. Acta
, vol.1818
, pp. 252-262
-
-
Im, W.1
Jo, S.2
Kim, T.3
-
41
-
-
11944266539
-
Information Theory and Statistical Mechanics
-
Jaynes, E. T. Information Theory and Statistical Mechanics Phys. Rev. 1957, 106, 620-630
-
(1957)
Phys. Rev.
, vol.106
, pp. 620-630
-
-
Jaynes, E.T.1
-
42
-
-
84874919387
-
On the Statistical Equivalence of Restrained-Ensemble Simulations with the Maximum Entropy Method
-
Roux, B.; Weare, J. On the Statistical Equivalence of Restrained-Ensemble Simulations With the Maximum Entropy Method J. Chem. Phys. 2013, 138, 084107
-
(2013)
J. Chem. Phys.
, vol.138
, pp. 084107
-
-
Roux, B.1
Weare, J.2
-
43
-
-
84877018294
-
Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron-Electron Resonance Spectroscopy
-
10.1021/jp3110369
-
Roux, B.; Islam, S. M. Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron-Electron Resonance Spectroscopy J. Phys. Chem. B 2013, 10.1021/jp3110369
-
(2013)
J. Phys. Chem. B
-
-
Roux, B.1
Islam, S.M.2
-
44
-
-
0037112592
-
Distance Measurements in the Nanometer Range by Pulse EPR
-
Jeschke, G. Distance Measurements in the Nanometer Range by Pulse EPR Chemphyschem 2002, 3, 927-932
-
(2002)
Chemphyschem
, vol.3
, pp. 927-932
-
-
Jeschke, G.1
-
45
-
-
33846344623
-
DeerAnalysis2006 - A Comprehensive Software Package for Analyzing Pulsed ELDOR Data
-
Jeschke, G.; Chechik, V.; Ionita, P.; Godt, A.; Zimmermann, H.; Banham, J.; Timmel, C. R.; Hilger, D.; Jung, H. DeerAnalysis2006-A Comprehensive Software Package for Analyzing Pulsed ELDOR Data Appl. Magn. Reson. 2006, 30, 473-499
-
(2006)
Appl. Magn. Reson.
, vol.30
, pp. 473-499
-
-
Jeschke, G.1
Chechik, V.2
Ionita, P.3
Godt, A.4
Zimmermann, H.5
Banham, J.6
Timmel, C.R.7
Hilger, D.8
Jung, H.9
-
46
-
-
11344285129
-
The Determination of Pair Distance Distributions by Pulsed ESR using Tikhonov Regularization
-
Chiang, Y. W.; Borbat, P. P.; Freed, J. H. The Determination of Pair Distance Distributions by Pulsed ESR using Tikhonov Regularization J. Magn. Reson. 2005, 172, 279-295
-
(2005)
J. Magn. Reson.
, vol.172
, pp. 279-295
-
-
Chiang, Y.W.1
Borbat, P.P.2
Freed, J.H.3
-
47
-
-
67650500988
-
CHARMM: 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. CHARMM: 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
-
48
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
49
-
-
0041784950
-
All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-1616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-1616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
50
-
-
3142714765
-
Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations
-
Mackerell, A. D.; Feig, M.; Brooks, C. L. Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations J. Comput. Chem. 2004, 25, 1400-1415
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
MacKerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
51
-
-
0023104358
-
Structure of Bacteriophage-T4 Lysozyme Refined at 1.7 a Resolution
-
Weaver, L. H.; Matthews, B. W. Structure of Bacteriophage-T4 Lysozyme Refined at 1.7 a Resolution J. Mol. Biol. 1987, 193, 189-199
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 189-199
-
-
Weaver, L.H.1
Matthews, B.W.2
-
52
-
-
36449006131
-
Modeling Side-Chains in Peptides and Proteins - Application of the Locally Enhanced Sampling and the Simulated Annealing Methods to Find Minimum Energy Conformations
-
Roitberg, A.; Elber, R. Modeling Side-Chains in Peptides and Proteins-Application of the Locally Enhanced Sampling and the Simulated Annealing Methods to Find Minimum Energy Conformations J. Chem. Phys. 1991, 95, 9277-9287
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 9277-9287
-
-
Roitberg, A.1
Elber, R.2
-
53
-
-
0033828425
-
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1
-
Simmerling, C.; Lee, M. R.; Ortiz, A. R.; Kolinski, A.; Skolnick, J.; Kollman, P. A. Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1 J. Am. Chem. Soc. 2000, 122, 8392-8402
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 8392-8402
-
-
Simmerling, C.1
Lee, M.R.2
Ortiz, A.R.3
Kolinski, A.4
Skolnick, J.5
Kollman, P.A.6
-
54
-
-
0032540692
-
Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the Alpha → Beta Anomerization of Glucose
-
Simmerling, C.; Fox, T.; Kollman, P. A. Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the Alpha → Beta Anomerization of Glucose J. Am. Chem. Soc. 1998, 120, 5771-5782
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 5771-5782
-
-
Simmerling, C.1
Fox, T.2
Kollman, P.A.3
-
55
-
-
36749113534
-
Generalized Langevin Equation Approach for Atom-Solid-Surface Scattering - General Formulation for Classical Scattering off Harmonic Solids
-
Adelman, S. A.; Doll, J. D. Generalized Langevin Equation Approach for Atom-Solid-Surface Scattering-General Formulation for Classical Scattering Off Harmonic Solids J. Chem. Phys. 1976, 64, 2375-2388
-
(1976)
J. Chem. Phys.
, vol.64
, pp. 2375-2388
-
-
Adelman, S.A.1
Doll, J.D.2
-
56
-
-
33646940952
-
Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints-Molecular-Dynamics of N-Alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
57
-
-
33846823909
-
Particle Mesh Ewald - An N.Log(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-An N.Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
58
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
59
-
-
0025600834
-
Enhanced Sampling in Molecular-Dynamics - Use of the Time-Dependent Hartree Approximation for a Simulation of Carbon-Monoxide Diffusion through Myoglobin
-
Elber, R.; Karplus, M. Enhanced Sampling in Molecular-Dynamics-Use of the Time-Dependent Hartree Approximation for a Simulation of Carbon-Monoxide Diffusion through Myoglobin J. Am. Chem. Soc. 1990, 112, 9161-9175
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 9161-9175
-
-
Elber, R.1
Karplus, M.2
-
60
-
-
0029878720
-
VMD: Visual Molecular Dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graph. 1996, 14, 33-38
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
61
-
-
84858332577
-
Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme
-
Georgieva, E. R.; Roy, A. S.; Grigoryants, V. M.; Borbat, P. P.; Earle, K. A.; Scholes, C. P.; Freed, J. H. Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme J. Magn. Reson. 2012, 216, 69-77
-
(2012)
J. Magn. Reson.
, vol.216
, pp. 69-77
-
-
Georgieva, E.R.1
Roy, A.S.2
Grigoryants, V.M.3
Borbat, P.P.4
Earle, K.A.5
Scholes, C.P.6
Freed, J.H.7
-
62
-
-
37049014272
-
Version 1.2 of the Crystallography and NMR System
-
Brunger, A. T. Version 1.2 of the Crystallography and NMR System Nat. Protoc. 2007, 2, 2728-2733
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2728-2733
-
-
Brunger, A.T.1
-
63
-
-
0041154173
-
Motion of Spin-Labeled Side Chains in T4 Lysozyme: Effect of Side Chain Structure
-
Mchaourab, H. S.; Kalai, T.; Hideg, K.; Hubbell, W. L. Motion of Spin-Labeled Side Chains in T4 Lysozyme: Effect of Side Chain Structure Biochemistry 1999, 38, 2947-2955
-
(1999)
Biochemistry
, vol.38
, pp. 2947-2955
-
-
McHaourab, H.S.1
Kalai, T.2
Hideg, K.3
Hubbell, W.L.4
-
64
-
-
47149096704
-
CHARMM-GUI: A Web-based Graphical User Interface for CHARMM
-
Jo, S.; Kim, T.; Iyer, V. G.; Im, W. CHARMM-GUI: A Web-based Graphical User Interface for CHARMM J. Comput. Chem. 2008, 29, 1859-1865
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1859-1865
-
-
Jo, S.1
Kim, T.2
Iyer, V.G.3
Im, W.4
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