-
1
-
-
18344385532
-
NMR spectroscopy and protein structure determination: Applications to drug discovery and development
-
Wishart DS (2005) NMR spectroscopy and protein structure determination: Applications to drug discovery and development. Curr Pharm Biotechnol 6: 105-120.
-
(2005)
Curr Pharm Biotechnol
, vol.6
, pp. 105-120
-
-
Wishart, D.S.1
-
2
-
-
20044390069
-
Recent developments in structural proteomics for protein structure determination
-
Liu HL, Hsu JP (2005) Recent developments in structural proteomics for protein structure determination. Proteomics 5: 2056-2068.
-
(2005)
Proteomics
, vol.5
, pp. 2056-2068
-
-
Liu, H.L.1
Hsu, J.P.2
-
3
-
-
4744344737
-
Automation of NMR structure determination of proteins
-
Altieri AS, Byrd RA (2004) Automation of NMR structure determination of proteins. Curr Opin Struct Biol 14: 547-553.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 547-553
-
-
Altieri, A.S.1
Byrd, R.A.2
-
4
-
-
3943074512
-
Nuclear magnetic resonance spectroscopy of highmolecular-weight proteins
-
Tugarinov V, Hwang PM, Kay LE (2004) Nuclear magnetic resonance spectroscopy of highmolecular-weight proteins. Annu Rev Biochem 73: 107-146.
-
(2004)
Annu Rev Biochem
, vol.73
, pp. 107-146
-
-
Tugarinov, V.1
Hwang, P.M.2
Kay, L.E.3
-
5
-
-
34748876721
-
Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings
-
Bouvignies G, Markwick PRL, Blackledge MJ (2007) Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings. Chemphyschem 8: 1901-1909.
-
(2007)
Chemphyschem
, vol.8
, pp. 1901-1909
-
-
Bouvignies, G.1
Markwick, P.R.L.2
Blackledge, M.J.3
-
7
-
-
33646356250
-
Detecting transient intermediates in macromolecular binding by paramagnetic NMR
-
Iwahara J, Clore GM (2006) Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440: 1227-1230.
-
(2006)
Nature
, vol.440
, pp. 1227-1230
-
-
Iwahara, J.1
Clore, G.M.2
-
9
-
-
0030722243
-
Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
-
Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278: 1111-1114.
-
(1997)
Science
, vol.278
, pp. 1111-1114
-
-
Tjandra, N.1
Bax, A.2
-
10
-
-
0034923356
-
Use of chemical shifts in macromolecular structure determination
-
Wishart DS, Case DA (2001) Use of chemical shifts in macromolecular structure determination. Methods Enzymol 338: 3-34.
-
(2001)
Methods Enzymol
, vol.338
, pp. 3-34
-
-
Wishart, D.S.1
Case, D.A.2
-
12
-
-
42449146665
-
Consistent blind protein structure generation from NMR chemical shift data
-
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, et al. (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A 105: 4685-4690.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 4685-4690
-
-
Shen, Y.1
Lange, O.2
Delaglio, F.3
Rossi, P.4
Aramini, J.M.5
-
13
-
-
0037038365
-
Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy
-
Castellani F, van Rossum B, Diehl A, Schubert M, Rehbein K, et al. (2002) Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Nature 420: 98-102.
-
(2002)
Nature
, vol.420
, pp. 98-102
-
-
Castellani, F.1
van Rossum, B.2
Diehl, A.3
Schubert, M.4
Rehbein, K.5
-
14
-
-
41449096392
-
3D structure determination of the crh protein from highly ambiguous solid-state NMR restraints
-
Loquet A, Bardiaux B, Gardiennet C, Blancher C, Baldus M, et al. (2008) 3D structure determination of the crh protein from highly ambiguous solid-state NMR restraints. JACS. pp 3579-3589.
-
(2008)
JACS
, pp. 3579-3589
-
-
Loquet, A.1
Bardiaux, B.2
Gardiennet, C.3
Blancher, C.4
Baldus, M.5
-
16
-
-
4644340524
-
Automated NMR structure calculation with CYANA
-
Güntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278: 353-378.
-
(2004)
Methods Mol Biol
, vol.278
, pp. 353-378
-
-
Güntert, P.1
-
17
-
-
33644774471
-
Optimal isotope labelling for NMR protein structure determinations
-
Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, et al. (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440: 52-57.
-
(2006)
Nature
, vol.440
, pp. 52-57
-
-
Kainosho, M.1
Torizawa, T.2
Iwashita, Y.3
Terauchi, T.4
Ono, A.M.5
-
18
-
-
19444382397
-
The CCPN data model for NMR spectroscopy: Development of a software pipeline
-
Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, et al. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59: 687-696.
-
(2005)
Proteins
, vol.59
, pp. 687-696
-
-
Vranken, W.F.1
Boucher, W.2
Stevens, T.J.3
Fogh, R.H.4
Pajon, A.5
-
19
-
-
16244377434
-
An integrated platform for automated analysis of protein NMR structures
-
Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, et al. (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 394: 111-141.
-
(2005)
Methods Enzymol
, vol.394
, pp. 111-141
-
-
Huang, Y.J.1
Moseley, H.N.2
Baran, M.C.3
Arrowsmith, C.4
Powers, R.5
-
20
-
-
2442717620
-
Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments
-
Kuszewski J, Schwieters CD, Garrett DS, Byrd RA, Tjandra N, et al. (2004) Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments. J Am Chem Soc 126: 6258-6273.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 6258-6273
-
-
Kuszewski, J.1
Schwieters, C.D.2
Garrett, D.S.3
Byrd, R.A.4
Tjandra, N.5
-
21
-
-
33847283016
-
ARIA2: Automated NOE assignment and data integration in NMR structure calculation
-
Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, et al. (2007) ARIA2: Automated NOE assignment and data integration in NMR structure calculation. Bioinformatics 23: 381-382.
-
(2007)
Bioinformatics
, vol.23
, pp. 381-382
-
-
Rieping, W.1
Habeck, M.2
Bardiaux, B.3
Bernard, A.4
Malliavin, T.E.5
-
22
-
-
0036308102
-
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
-
Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319: 209-227.
-
(2002)
J Mol Biol
, vol.319
, pp. 209-227
-
-
Herrmann, T.1
Güntert, P.2
Wüthrich, K.3
-
23
-
-
31944451135
-
A topology-constrained distance network algorithm for protein structure determination from NOESY data
-
Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins 62: 587-603.
-
(2006)
Proteins
, vol.62
, pp. 587-603
-
-
Huang, Y.J.1
Tejero, R.2
Powers, R.3
Montelione, G.T.4
-
24
-
-
4644234334
-
Mars - Robust automatic backbone assignment of proteins
-
Jung YS, Zweckstetter M (2004) Mars - Robust automatic backbone assignment of proteins. J Biomol NMR 30: 11-23.
-
(2004)
J Biomol NMR
, vol.30
, pp. 11-23
-
-
Jung, Y.S.1
Zweckstetter, M.2
-
25
-
-
33749524593
-
Automated protein structure determination from NMR spectra
-
Lopez-Mendez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128: 13112-13122.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 13112-13122
-
-
Lopez-Mendez, B.1
Güntert, P.2
-
26
-
-
16244420047
-
Protein structure elucidation from minimal NMR data: The CLOUDS approach
-
Grishaev A, Llinas M (2005) Protein structure elucidation from minimal NMR data: The CLOUDS approach. Methods Enzymol 394: 261-295.
-
(2005)
Methods Enzymol
, vol.394
, pp. 261-295
-
-
Grishaev, A.1
Llinas, M.2
-
27
-
-
33745096027
-
Direct use of unassigned resonances in NMR structure calculations with proxy residues
-
Ab E, Pugh DJ, Kaptein R, Boelens R, Bonvin AM (2006) Direct use of unassigned resonances in NMR structure calculations with proxy residues. J Am Chem Soc 128: 7566-7571.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 7566-7571
-
-
Ab, E.1
Pugh, D.J.2
Kaptein, R.3
Boelens, R.4
Bonvin, A.M.5
-
28
-
-
0035925135
-
Determination of protein backbone structure using only residual dipolar couplings
-
Hus JC, Marion D, Blackledge M (2001) Determination of protein backbone structure using only residual dipolar couplings. J Am Chem Soc 123: 1541-1542.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 1541-1542
-
-
Hus, J.C.1
Marion, D.2
Blackledge, M.3
-
29
-
-
16244404569
-
Molecular fragment replacement approach to protein structure determination by chemical shift and dipolar homology database mining
-
Kontaxis G, Delaglio F, Bax A (2005) Molecular fragment replacement approach to protein structure determination by chemical shift and dipolar homology database mining. Methods Enzymol 394: 42-78.
-
(2005)
Methods Enzymol
, vol.394
, pp. 42-78
-
-
Kontaxis, G.1
Delaglio, F.2
Bax, A.3
-
30
-
-
33846263054
-
A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data
-
Wang L, Mettu RR, Donald BR (2006) A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. J Comput Biol 13: 1267-1288.
-
(2006)
J Comput Biol
, vol.13
, pp. 1267-1288
-
-
Wang, L.1
Mettu, R.R.2
Donald, B.R.3
-
31
-
-
0346103679
-
Rapid protein fold determination using unassigned NMR data
-
Meiler J, Baker D (2003) Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci U S A 100: 15404-15409.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 15404-15409
-
-
Meiler, J.1
Baker, D.2
-
32
-
-
0037433504
-
15N chemical shift mapping and backbone 15n-1h residual dipolar couplings using conjoined rigid body/torsion angle dynamics
-
15N chemical shift mapping and backbone 15n-1h residual dipolar couplings using conjoined rigid body/torsion angle dynamics. J Am Chem Soc 125: 2902-2912.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 2902-2912
-
-
Clore, G.M.1
Schwieters, C.D.2
-
33
-
-
28444453002
-
Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data
-
Grishaev A, Wu J, Trewhella J, Bax A (2005) Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. J Am Chem Soc 127: 16621-16628.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 16621-16628
-
-
Grishaev, A.1
Wu, J.2
Trewhella, J.3
Bax, A.4
-
34
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin A (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731-1737.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.3
-
35
-
-
33750371561
-
Proton-proton Overhauser NMR spectroscopy with polypeptide chains in large structures
-
Horst R, Wider G, Fiaux J, Bertelsen EB, Horwich AL, et al. (2006) Proton-proton Overhauser NMR spectroscopy with polypeptide chains in large structures. Proc Natl Acad Sci U S A 103: 15445-15450.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 15445-15450
-
-
Horst, R.1
Wider, G.2
Fiaux, J.3
Bertelsen, E.B.4
Horwich, A.L.5
-
36
-
-
33846928691
-
Quantitative dynamics and binding studies of the 20S proteasome by NMR
-
Sprangers R, Kay LE (2007) Quantitative dynamics and binding studies of the 20S proteasome by NMR. Nature 445: 618-622.
-
(2007)
Nature
, vol.445
, pp. 618-622
-
-
Sprangers, R.1
Kay, L.E.2
-
37
-
-
20144384787
-
Solution NMR structure of the 48-kda IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system
-
Williams DC Jr, Cai M, Suh JY, Peterkofsky A, Clore GM (2005) Solution NMR structure of the 48-kda IIAMannose-HPr complex of the Escherichia coli mannose phosphotransferase system. J Biol Chem 280: 20775-20784.
-
(2005)
J Biol Chem
, vol.280
, pp. 20775-20784
-
-
Williams Jr, D.C.1
Cai, M.2
Suh, J.Y.3
Peterkofsky, A.4
Clore, G.M.5
-
38
-
-
33751086423
-
Visualization of transient encounter complexes in protein-protein association
-
Tang C, Iwahara J, Clore GM (2006) Visualization of transient encounter complexes in protein-protein association. Nature 444: 383-386.
-
(2006)
Nature
, vol.444
, pp. 383-386
-
-
Tang, C.1
Iwahara, J.2
Clore, G.M.3
-
39
-
-
33847079676
-
Evaluating protein structures determined by structural genomics consortia
-
Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66: 778-795.
-
(2007)
Proteins
, vol.66
, pp. 778-795
-
-
Bhattacharya, A.1
Tejero, R.2
Montelione, G.T.3
-
40
-
-
0141508959
-
Quantitative evaluation of experimental NMR restraints
-
Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, et al. (2003) Quantitative evaluation of experimental NMR restraints. J Am Chem Soc 125: 12026-12034.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 12026-12034
-
-
Nabuurs, S.B.1
Spronk, C.A.2
Krieger, E.3
Maassen, H.4
Vriend, G.5
-
41
-
-
22144489530
-
Inferential structure determination
-
Rieping W, Habeck M, Nilges M (2005) Inferential structure determination. Science 309: 303-306.
-
(2005)
Science
, vol.309
, pp. 303-306
-
-
Rieping, W.1
Habeck, M.2
Nilges, M.3
-
42
-
-
33751332985
-
Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation
-
Nicastro G, Habeck M, Masino L, Svergun DI, Pastore A (2006) Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation. J Biomol NMR 36: 267-277.
-
(2006)
J Biomol NMR
, vol.36
, pp. 267-277
-
-
Nicastro, G.1
Habeck, M.2
Masino, L.3
Svergun, D.I.4
Pastore, A.5
-
43
-
-
13644252170
-
Protein NMR recall, precision, and f-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics
-
Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and f-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127: 1665-1674.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 1665-1674
-
-
Huang, Y.J.1
Powers, R.2
Montelione, G.T.3
-
44
-
-
0037441524
-
Refinement of protein structures in explicit solvent
-
Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50: 496-506.
-
(2003)
Proteins
, vol.50
, pp. 496-506
-
-
Linge, J.P.1
Williams, M.A.2
Spronk, C.A.3
Bonvin, A.M.4
Nilges, M.5
-
45
-
-
21044449889
-
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, et al. (2005) RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59: 662-672.
-
(2005)
Proteins
, vol.59
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
Miller, Z.4
Spronk, C.A.5
-
46
-
-
84918314491
-
Refinement of large structures by simultaneous minimization of energy and R factor
-
Jack A, Levitt M (1978) Refinement of large structures by simultaneous minimization of energy and R factor. Acta Cryst A34: 931-935.
-
(1978)
Acta Cryst
, vol.A34
, pp. 931-935
-
-
Jack, A.1
Levitt, M.2
-
47
-
-
0027293559
-
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy
-
Brunger AT, Nilges M (1993) Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy. Quart Rev BioPhys 26: 49-125.
-
(1993)
Quart Rev BioPhys
, vol.26
, pp. 49-125
-
-
Brunger, A.T.1
Nilges, M.2
-
48
-
-
0037357143
-
The precision of NMR structure ensembles revisited
-
Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, et al. (2003) The precision of NMR structure ensembles revisited. J Biomol NMR 25: 225-234.
-
(2003)
J Biomol NMR
, vol.25
, pp. 225-234
-
-
Spronk, C.A.1
Nabuurs, S.B.2
Bonvin, A.M.3
Krieger, E.4
Vuister, G.W.5
-
49
-
-
18844415920
-
Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
-
Snyder DA, Montelione GT (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins 59: 673-686.
-
(2005)
Proteins
, vol.59
, pp. 673-686
-
-
Snyder, D.A.1
Montelione, G.T.2
-
50
-
-
33645790319
-
Traditional biomolecular structure determination by NMR spectroscopy allows for major errors
-
doi:10.1371/journal.pcbi.0020009
-
Nabuurs SB, Spronk CA, Vuister GW, Vriend G (2006) Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2: e9. doi:10.1371/journal.pcbi.0020009.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Nabuurs, S.B.1
Spronk, C.A.2
Vuister, G.W.3
Vriend, G.4
-
51
-
-
32444439415
-
Weighting of experimental evidence in macromolecular structure determination
-
Habeck M, Rieping W, Nilges M (2006) Weighting of experimental evidence in macromolecular structure determination. Proc Natl Acad Sci U S A 103: 1756-1761.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 1756-1761
-
-
Habeck, M.1
Rieping, W.2
Nilges, M.3
-
52
-
-
18144399340
-
Replica-exchange Monte Carlo scheme for Bayesian data analysis
-
Habeck M, Nilges M, Rieping W (2005) Replica-exchange Monte Carlo scheme for Bayesian data analysis. Phys Rev Lett 94: 018105.
-
(2005)
Phys Rev Lett
, vol.94
, pp. 018105
-
-
Habeck, M.1
Nilges, M.2
Rieping, W.3
-
53
-
-
0024435205
-
A dynamic model for the structure of acyl carrier protein in solution
-
Kim Y, Prestegard JH (1989) A dynamic model for the structure of acyl carrier protein in solution. Biochemistry 28: 8792-8797.
-
(1989)
Biochemistry
, vol.28
, pp. 8792-8797
-
-
Kim, Y.1
Prestegard, J.H.2
-
54
-
-
0025367860
-
Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat
-
Torda AE, Scheek RM, van Gunsteren WF (1990) Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. J Mol Biol 214: 223-235.
-
(1990)
J Mol Biol
, vol.214
, pp. 223-235
-
-
Torda, A.E.1
Scheek, R.M.2
van Gunsteren, W.F.3
-
55
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 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
-
56
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450: 913-916.
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
-
57
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
-
Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104: 4546-4559.
-
(1982)
J Am Chem Soc
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
58
-
-
36849125639
-
Nuclear magnetic dipole-dipole relaxation in molecules with internal motion
-
Woessner DE (1965) Nuclear magnetic dipole-dipole relaxation in molecules with internal motion. J Chem Phys 42: 1855-1859.
-
(1965)
J Chem Phys
, vol.42
, pp. 1855-1859
-
-
Woessner, D.E.1
-
59
-
-
0346159350
-
Motional model analyses of protein and peptide dynamics using 13C and 15N NMR relaxation
-
Daragan VA, Mayo KH (1997) Motional model analyses of protein and peptide dynamics using 13C and 15N NMR relaxation. Prog NMR Spectrosc 31: 63-105.
-
(1997)
Prog NMR Spectrosc
, vol.31
, pp. 63-105
-
-
Daragan, V.A.1
Mayo, K.H.2
-
60
-
-
0035930040
-
Molecular dynamics and NMR spin relaxation in proteins
-
Chang SL, Tiandra N (2001) Molecular dynamics and NMR spin relaxation in proteins. J Am Chem Soc 123: 11484-11485.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 11484-11485
-
-
Chang, S.L.1
Tiandra, N.2
-
61
-
-
0030752071
-
Locally anisotropic internal polypeptide backbone dynamics by NMR relaxation
-
Bremi T, Bruschweiler R (1997) Locally anisotropic internal polypeptide backbone dynamics by NMR relaxation. J Am Chem Soc 119: 6672-6673.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 6672-6673
-
-
Bremi, T.1
Bruschweiler, R.2
-
62
-
-
0037202183
-
Contact model for the prediction of NMR NH order parameters in globular proteins
-
Zhang F, Brüschweiler R (2002) Contact model for the prediction of NMR NH order parameters in globular proteins. J Am Chem Soc 124: 12654-12655.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 12654-12655
-
-
Zhang, F.1
Brüschweiler, R.2
-
63
-
-
28344437280
-
Predicting internal protein dynamics from structures using coupled networks of hindered rotators
-
Abergel D, Bodenhausen G (2005) Predicting internal protein dynamics from structures using coupled networks of hindered rotators. J Chem Phys 123: 204901.
-
(2005)
J Chem Phys
, vol.123
, pp. 204901
-
-
Abergel, D.1
Bodenhausen, G.2
-
64
-
-
0037398803
-
New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins
-
Bruschweiler R (2003) New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Curr Opion Struct Biol 13: 175-183.
-
(2003)
Curr Opion Struct Biol
, vol.13
, pp. 175-183
-
-
Bruschweiler, R.1
-
65
-
-
4544283595
-
Site-specific variations of cabonyl chemical shift anisotropies in proteins
-
Markwick PRL, Sattler M (2004) Site-specific variations of cabonyl chemical shift anisotropies in proteins. J Am Chem Soc 126: 11424-11425.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 11424-11425
-
-
Markwick, P.R.L.1
Sattler, M.2
-
66
-
-
20344379472
-
Local structure and anisotropic backbone dynamics from cross-correlated NMR relaxation in proteins
-
Markwick PRL, Sprangers R, Sattler M (2005) Local structure and anisotropic backbone dynamics from cross-correlated NMR relaxation in proteins. Ang Chem Int Ed 44: 3232-3237.
-
(2005)
Ang Chem Int Ed
, vol.44
, pp. 3232-3237
-
-
Markwick, P.R.L.1
Sprangers, R.2
Sattler, M.3
-
67
-
-
0036283096
-
Molecular dynamics and NMR spin relaxation in proteins
-
Case DA (2002) Molecular dynamics and NMR spin relaxation in proteins. Acc Chem Res 35: 325-331.
-
(2002)
Acc Chem Res
, vol.35
, pp. 325-331
-
-
Case, D.A.1
-
68
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
Mackerell AD Jr (2004) Empirical force fields for biological macromolecules: Overview and issues. J Comput Chem 25: 1584-1604.
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
Mackerell Jr, A.D.1
-
69
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Struct Funct Bioinf 65: 712-725.
-
(2006)
Proteins: Struct Funct Bioinf
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
-
70
-
-
34247500337
-
Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy
-
Markwick PR, Bouvignies G, Blackledge M (2007) Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J Am Chem Soc 129: 4724-4730.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 4724-4730
-
-
Markwick, P.R.1
Bouvignies, G.2
Blackledge, M.3
-
71
-
-
17744366182
-
Chemical shift anisotropy tensors of carbonyl, nitrogen and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy
-
Loth K, Pelupessy P, Bodenhausen G (2005) Chemical shift anisotropy tensors of carbonyl, nitrogen and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy. J Am Chem Soc 127: 6062-6068.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 6062-6068
-
-
Loth, K.1
Pelupessy, P.2
Bodenhausen, G.3
-
72
-
-
0034829466
-
A structural mode-coupling approach to 15N NMR relaxation in proteins
-
Tugarinov V, Liang Z, Shapiro YE, Freed JH, Meirovitch E (2001) A structural mode-coupling approach to 15N NMR relaxation in proteins. J Am Chem Soc 123: 3055-3063.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 3055-3063
-
-
Tugarinov, V.1
Liang, Z.2
Shapiro, Y.E.3
Freed, J.H.4
Meirovitch, E.5
-
73
-
-
0042367594
-
Evaluation of backbone proton postions and dynamics in a small protein by liquid crystal NMR spectroscopy
-
Ulmer TA, Ramirez BE, Delaglio F, Bax A (2003) Evaluation of backbone proton postions and dynamics in a small protein by liquid crystal NMR spectroscopy. J Am Chem Soc 125: 9179-9191.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 9179-9191
-
-
Ulmer, T.A.1
Ramirez, B.E.2
Delaglio, F.3
Bax, A.4
-
74
-
-
1542317796
-
How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?
-
Clore GM, Schwieters CD (2004) How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J Am Chem Soc 126: 2923-2938.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 2923-2938
-
-
Clore, G.M.1
Schwieters, C.D.2
-
75
-
-
0037157093
-
Model-free analysis of protein backbone motion from residual dipolar couplings
-
Peti W, Meiler J, Bruschweiler R, Griesinger C (2002) Model-free analysis of protein backbone motion from residual dipolar couplings. J Am Chem Soc 124: 5822-5833.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 5822-5833
-
-
Peti, W.1
Meiler, J.2
Bruschweiler, R.3
Griesinger, C.4
-
76
-
-
33645469988
-
A thorough dynamic interpretation of residual dipolar couplings in ubiquitin
-
Lakomek NA, Carlomagno T, Becker S, Griesinger C (2006) A thorough dynamic interpretation of residual dipolar couplings in ubiquitin. J Biomol NMR 34: 101-115.
-
(2006)
J Biomol NMR
, vol.34
, pp. 101-115
-
-
Lakomek, N.A.1
Carlomagno, T.2
Becker, S.3
Griesinger, C.4
-
77
-
-
0042933782
-
De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy
-
Briggman KB, Tolman JR (2003) De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy. J Am Chem Soc 125: 10164-10165.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 10164-10165
-
-
Briggman, K.B.1
Tolman, J.R.2
-
78
-
-
25444532318
-
Identification of slow correlated motions in proteins using residual dipolar couplings and hydrogen-bond scaler couplings
-
Bouvignies G, Bernado P, Meier S, Cho K, Grzesiek S, et al. (2005) Identification of slow correlated motions in proteins using residual dipolar couplings and hydrogen-bond scaler couplings. Proc Nat Acad Sci 102: 13885-13890.
-
(2005)
Proc Nat Acad Sci
, vol.102
, pp. 13885-13890
-
-
Bouvignies, G.1
Bernado, P.2
Meier, S.3
Cho, K.4
Grzesiek, S.5
-
79
-
-
33845203743
-
Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings
-
Bouvignies G, Markwick PRL, Bruschweiler R, Blackledge M (2006) Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings. J Am Chem Soc 128: 15100-15101.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 15100-15101
-
-
Bouvignies, G.1
Markwick, P.R.L.2
Bruschweiler, R.3
Blackledge, M.4
-
80
-
-
36749058463
-
Measurement of bond vector orientations in invisible excited states of proteins
-
Vallurupalli P, Hansen DF, Stollar E, Meirovitch E, Kay LE (2007) Measurement of bond vector orientations in invisible excited states of proteins. Proc Natl Acad Sci U S A 104: 18473-18477.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 18473-18477
-
-
Vallurupalli, P.1
Hansen, D.F.2
Stollar, E.3
Meirovitch, E.4
Kay, L.E.5
-
81
-
-
0033577288
-
A relaxation-compensated carr-purcell-meilboomgill sequence for characterizing chemical exchange by NMR spectroscopy
-
Loria JP, Rance M, Palmer AG (1999) A relaxation-compensated carr-purcell-meilboomgill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121: 2331-2332.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 2331-2332
-
-
Loria, J.P.1
Rance, M.2
Palmer, A.G.3
-
82
-
-
0030612833
-
Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution
-
Pervushin K, Riek R, Wider G, Wüthrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Nat Acad Sci U S A 94: 12366-12371.
-
(1997)
Proc Nat Acad Sci U S A
, vol.94
, pp. 12366-12371
-
-
Pervushin, K.1
Riek, R.2
Wider, G.3
Wüthrich, K.4
-
83
-
-
0035928796
-
Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
-
Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE (2001) Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism. Biochemistry 40: 9846-9859.
-
(2001)
Biochemistry
, vol.40
, pp. 9846-9859
-
-
Osborne, M.J.1
Schnell, J.2
Benkovic, S.J.3
Dyson, H.J.4
Wright, P.E.5
-
84
-
-
0037076522
-
Evidence for flexibility in the function of ribonuclease A
-
Cole R, Loria JP (2002) Evidence for flexibility in the function of ribonuclease A. Biochemistry 41: 6072-6081.
-
(2002)
Biochemistry
, vol.41
, pp. 6072-6081
-
-
Cole, R.1
Loria, J.P.2
-
86
-
-
0033566242
-
Millisecond-timescale motions contribute to the function of the bacterial response regulator protein SpoOF
-
Feher VA, Cavanagh J (1999) Millisecond-timescale motions contribute to the function of the bacterial response regulator protein SpoOF. Nature 400: 289-293.
-
(1999)
Nature
, vol.400
, pp. 289-293
-
-
Feher, V.A.1
Cavanagh, J.2
-
87
-
-
0034759979
-
Studying excited states of proteins by NMR spectroscopy
-
Mulder FAA, Mittermaier AA, Hon B, Dahlquist FW, Kay LE (2001) Studying excited states of proteins by NMR spectroscopy. Nat Struct Biol 8: 932-935.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 932-935
-
-
Mulder, F.A.A.1
Mittermaier, A.A.2
Hon, B.3
Dahlquist, F.W.4
Kay, L.E.5
-
88
-
-
0035937443
-
Two-state allosteric behaviour in a single-domain signaling protein
-
Volkman BF, Lipson D, Wemmer D, Kern D (2001) Two-state allosteric behaviour in a single-domain signaling protein. Science 291: 2429-2433.
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.3
Kern, D.4
-
89
-
-
3242880292
-
Lowpopulated folding intermediates of fyn sh3 characterized by relaxation dispersion NMR
-
Korzhnev DM, Salvatella X, Vendruscolo M, Nardo AAD, Davidson AR, et al. (2004) Lowpopulated folding intermediates of fyn sh3 characterized by relaxation dispersion NMR. Nature 430: 586-590.
-
(2004)
Nature
, vol.430
, pp. 586-590
-
-
Korzhnev, D.M.1
Salvatella, X.2
Vendruscolo, M.3
Nardo, A.A.D.4
Davidson, A.R.5
-
90
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438: 117-121.
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
-
91
-
-
40949113653
-
Probing structure in invisible protein states with anisotropic NMR chemical shifts
-
Vallurupalli P, Hansen DF, Kay LE (2008) Probing structure in invisible protein states with anisotropic NMR chemical shifts. J Am Chem Soc 130: 2734-2735.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 2734-2735
-
-
Vallurupalli, P.1
Hansen, D.F.2
Kay, L.E.3
-
92
-
-
0034945906
-
Functional dynamics in the active site of the ribonuclease binase
-
Wang L, Pang Y, Holder T, Brender JR, Kurochkin AV, et al. (2001) Functional dynamics in the active site of the ribonuclease binase. Proc Nat Acad Sci U S A 98: 7684-7689.
-
(2001)
Proc Nat Acad Sci U S A
, vol.98
, pp. 7684-7689
-
-
Wang, L.1
Pang, Y.2
Holder, T.3
Brender, J.R.4
Kurochkin, A.V.5
-
93
-
-
0000689085
-
Predicting slow structural transistions in macromolecular systems: Conformational flooding
-
Grubmüller H (1995) Predicting slow structural transistions in macromolecular systems: Conformational flooding. Phys Rev E 52: 2893-2907.
-
(1995)
Phys Rev E
, vol.52
, pp. 2893-2907
-
-
Grubmüller, H.1
-
94
-
-
3142716857
-
Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease
-
Hamelberg D, Mongan J, McCammon JA (2004) Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Chem Phys 120: 11919-11929.
-
(2004)
J Chem Phys
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
95
-
-
17044425870
-
Long-timescale simulation methods
-
Elber R (2005) Long-timescale simulation methods. Curr Opin Struct Biol 15: 151-156.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 151-156
-
-
Elber, R.1
-
96
-
-
0040488445
-
Functional significance of hierachical tiers in carbonmonoxy myoglobin: Conformational substates and transitions studied by conformational flooding simulations
-
Schulze BG, Grubmüller H, Evanseck JD (2000) Functional significance of hierachical tiers in carbonmonoxy myoglobin: Conformational substates and transitions studied by conformational flooding simulations. J Am Chem Soc 122: 8700-8711.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 8700-8711
-
-
Schulze, B.G.1
Grubmüller, H.2
Evanseck, J.D.3
-
97
-
-
26444548978
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
Hamelberg D, McCammon JA (2005) Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J Am Chem Soc 127: 13778-13779.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 13778-13779
-
-
Hamelberg, D.1
McCammon, J.A.2
-
98
-
-
28744436857
-
NMR relaxation and internal dynamics of ubiquitin from a 0.2 μs MD simulation
-
Nederveen AJ, Bonvin AMJJ (2005) NMR relaxation and internal dynamics of ubiquitin from a 0.2 μs MD simulation. J Chem Theory and Comput 1: 363-374.
-
(2005)
J Chem Theory and Comput
, vol.1
, pp. 363-374
-
-
Nederveen, A.J.1
Bonvin, A.M.J.J.2
-
99
-
-
14644435825
-
Intrinsically unstructured proteins and their functions
-
Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197-208.
-
(2005)
Nat Rev Mol Cell Biol
, vol.6
, pp. 197-208
-
-
Dyson, H.J.1
Wright, P.E.2
-
100
-
-
0035919635
-
Persistence of native-like topology in a denatured protein in 8 m urea
-
Shortle D, Ackerman MS (2001) Persistence of native-like topology in a denatured protein in 8 m urea. Science 293: 487-489.
-
(2001)
Science
, vol.293
, pp. 487-489
-
-
Shortle, D.1
Ackerman, M.S.2
-
101
-
-
28044458515
-
A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering
-
Bernardo P, Blanchard L, Timmins P, Marion D, Ruigrok WH, et al. (2005) A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. Proc Nat Acad Sci U S A 102: 17002-17007.
-
(2005)
Proc Nat Acad Sci U S A
, vol.102
, pp. 17002-17007
-
-
Bernardo, P.1
Blanchard, L.2
Timmins, P.3
Marion, D.4
Ruigrok, W.H.5
-
102
-
-
24944542708
-
Statistical coil model of the unfolded state: Resolving the reconciliation problem
-
Jha AK, Colubri A, Freed K, Sosnick T (2005) Statistical coil model of the unfolded state: Resolving the reconciliation problem. Proc Nat Acad Sci 102: 13099-13104.
-
(2005)
Proc Nat Acad Sci
, vol.102
, pp. 13099-13104
-
-
Jha, A.K.1
Colubri, A.2
Freed, K.3
Sosnick, T.4
-
103
-
-
34247499863
-
Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation
-
Mukrasch MD, Markwick PRL, Biernat J, von Bergen M, Bernado P, et al. (2007) Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation. J Am Chem Soc 129: 5235-5243.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 5235-5243
-
-
Mukrasch, M.D.1
Markwick, P.R.L.2
Biernat, J.3
von Bergen, M.4
Bernado, P.5
|