-
1
-
-
0021710076
-
Xenopus 5S gene transcription factor, TFIIIA: Characterization of a cDNA clone and measurement of RNA levels throughout development
-
A.M. Ginsberg B.O. King R.G. Roeder Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development Cell 39 1984 479 489
-
(1984)
Cell
, vol.39
, pp. 479-489
-
-
Ginsberg, A.M.1
King, B.O.2
Roeder, R.G.3
-
2
-
-
0040215628
-
Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes
-
J. Miller A.D. McLachlan A. Klug Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes EMBO J. 4 1985 1609 1614
-
(1985)
EMBO J.
, vol.4
, pp. 1609-1614
-
-
Miller, J.1
McLachlan, A.D.2
Klug, A.3
-
4
-
-
0029032723
-
Protein motifs 5. Zinc fingers
-
A. Klug J.W. Schwabe Protein motifs 5. Zinc fingers FASEB J. 9 1995 597 604
-
(1995)
FASEB J.
, vol.9
, pp. 597-604
-
-
Klug, A.1
Schwabe, J.W.2
-
6
-
-
13844297911
-
Zinc finger proteins: Getting a grip on RNA
-
R.S. Brown Zinc finger proteins: getting a grip on RNA Curr. Opin. Struct. Biol. 15 2005 94 98
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 94-98
-
-
Brown, R.S.1
-
11
-
-
0012487168
-
2 zinc finger motif
-
2 zinc finger motif Nucleic Acids Res. 30 2002 4945 4951
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4945-4951
-
-
Dathan, N.1
Zaccaro, L.2
Esposito, S.3
Isernia, C.4
Omichinski, J.G.5
Riccio, A.6
Pedone, C.7
Di Blasio, B.8
Fattorusso, R.9
Pedone, P.V.10
-
12
-
-
0037416495
-
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein
-
C. Isernia E. Bucci M. Leone L. Zaccaro P. Di Lello G. Digilio S. Esposito M. Saviano B. Di Blasio C. Pedone P.V. Pedone R. Fattorusso NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein Chembiochem 4 2003 171 180
-
(2003)
Chembiochem
, vol.4
, pp. 171-180
-
-
Isernia, C.1
Bucci, E.2
Leone, M.3
Zaccaro, L.4
Di Lello, P.5
Digilio, G.6
Esposito, S.7
Saviano, M.8
Di Blasio, B.9
Pedone, C.10
Pedone, P.V.11
Fattorusso, R.12
-
13
-
-
36849081773
-
2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain
-
2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain Proc. Natl. Acad. Sci. USA 104 2007 17341 17346
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 17341-17346
-
-
Malgieri, G.1
Russo, L.2
Esposito, S.3
Baglivo, I.4
Zaccaro, L.5
Pedone, E.M.6
Di Blasio, B.7
Isernia, C.8
Pedone, P.V.9
Fattorusso, R.10
-
14
-
-
66349098084
-
The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains
-
I. Baglivo L. Russo S. Esposito G. Malgieri M. Renda A. Salluzzo B. Di Blasio C. Isernia R. Fattorusso P.V. Pedone The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains Proc. Natl. Acad. Sci. USA 106 2009 6933 6938
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 6933-6938
-
-
Baglivo, I.1
Russo, L.2
Esposito, S.3
Malgieri, G.4
Renda, M.5
Salluzzo, A.6
Di Blasio, B.7
Isernia, C.8
Fattorusso, R.9
Pedone, P.V.10
-
15
-
-
84892910209
-
Molecular strategies to replace the structural metal site in the prokaryotic zinc finger domain
-
I. Baglivo M. Palmieri A. Rivellino F. Netti L. Russo S. Esposito R. Iacovino B. Farina C. Isernia R. Fattorusso P.V. Pedone G. Malgieri Molecular strategies to replace the structural metal site in the prokaryotic zinc finger domain Biochim. Biophys. Acta 1844 2014 497 504
-
(2014)
Biochim. Biophys. Acta
, vol.1844
, pp. 497-504
-
-
Baglivo, I.1
Palmieri, M.2
Rivellino, A.3
Netti, F.4
Russo, L.5
Esposito, S.6
Iacovino, R.7
Farina, B.8
Isernia, C.9
Fattorusso, R.10
Pedone, P.V.11
Malgieri, G.12
-
16
-
-
33748655014
-
A novel type of zinc finger DNA binding domain in the Agrobacterium tumefaciens transcriptional regulator Ros
-
S. Esposito I. Baglivo G. Malgieri L. Russo L. Zaccaro L.D. D'Andrea M. Mammucari B. Di Blasio C. Isernia R. Fattorusso P.V. Pedone A novel type of zinc finger DNA binding domain in the Agrobacterium tumefaciens transcriptional regulator Ros Biochemistry 45 2006 10394 10405
-
(2006)
Biochemistry
, vol.45
, pp. 10394-10405
-
-
Esposito, S.1
Baglivo, I.2
Malgieri, G.3
Russo, L.4
Zaccaro, L.5
D'Andrea, L.D.6
Mammucari, M.7
Di Blasio, B.8
Isernia, C.9
Fattorusso, R.10
Pedone, P.V.11
-
17
-
-
19544370004
-
Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray-and NMR-resolved protein structures?
-
S.O. Garbuzynskiy B.S. Melnik M.Y. Lobanov A.V. Finkelstein O.V. Galzitskaya Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray-and NMR-resolved protein structures? Proteins 60 2005 139 147
-
(2005)
Proteins
, vol.60
, pp. 139-147
-
-
Garbuzynskiy, S.O.1
Melnik, B.S.2
Lobanov, M.Y.3
Finkelstein, A.V.4
Galzitskaya, O.V.5
-
18
-
-
0037398803
-
New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins
-
R. Brüschweiler New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins Curr. Opin. Struct. Biol. 13 2003 175 183
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 175-183
-
-
Brüschweiler, R.1
-
21
-
-
33947411739
-
A model of interdomain mobility in a multidomain protein
-
Y.E. Ryabov D. Fushman A model of interdomain mobility in a multidomain protein J. Am. Chem. Soc. 129 2007 3315 3327
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 3315-3327
-
-
Ryabov, Y.E.1
Fushman, D.2
-
22
-
-
0034789588
-
Analysis of slow interdomain motion of macromolecules using NMR relaxation data
-
J.L. Baber A. Szabo N. Tjandra Analysis of slow interdomain motion of macromolecules using NMR relaxation data J. Am. Chem. Soc. 123 2001 3953 3959
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3953-3959
-
-
Baber, J.L.1
Szabo, A.2
Tjandra, N.3
-
23
-
-
0034820148
-
Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins
-
J. Meiler J.J. Prompers W. Peti C. Griesinger R. Brüschweiler Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins J. Am. Chem. Soc. 123 2001 6098 6107
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 6098-6107
-
-
Meiler, J.1
Prompers, J.J.2
Peti, W.3
Griesinger, C.4
Brüschweiler, R.5
-
25
-
-
33845923184
-
Efficient molecular docking of NMR structures: Application to HIV-1 protease
-
S.Y. Huang X. Zou Efficient molecular docking of NMR structures: application to HIV-1 protease Protein Sci. 16 2007 43 51
-
(2007)
Protein Sci.
, vol.16
, pp. 43-51
-
-
Huang, S.Y.1
Zou, X.2
-
26
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
M. Karplus J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
27
-
-
80054950510
-
Molecular dynamics simulations and drug discovery
-
J.D. Durrant J.A. McCammon Molecular dynamics simulations and drug discovery BMC Biol. 9 2011 71
-
(2011)
BMC Biol.
, vol.9
, pp. 71
-
-
Durrant, J.D.1
McCammon, J.A.2
-
29
-
-
27544456339
-
A simple method to predict protein flexibility using secondary chemical shifts
-
M.V. Berjanskii D.S. Wishart A simple method to predict protein flexibility using secondary chemical shifts J. Am. Chem. Soc. 127 2005 14970 14971
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 14970-14971
-
-
Berjanskii, M.V.1
Wishart, D.S.2
-
30
-
-
34547563370
-
The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts
-
M.V. Berjanskii D.S. Wishart The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts Nucleic Acids Res. 35 2007 W531 W537
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 531-W537
-
-
Berjanskii, M.V.1
Wishart, D.S.2
-
31
-
-
33751552347
-
Sensitivity of secondary structure propensities to sequence differences between alpha-and gamma-synuclein: Implications for fibrillation
-
J.A. Marsh V.K. Singh Z. Jia J.D. Forman-Kay Sensitivity of secondary structure propensities to sequence differences between alpha-and gamma-synuclein: implications for fibrillation Protein Sci. 15 2006 2795 2804
-
(2006)
Protein Sci.
, vol.15
, pp. 2795-2804
-
-
Marsh, J.A.1
Singh, V.K.2
Jia, Z.3
Forman-Kay, J.D.4
-
32
-
-
72449187567
-
DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure
-
M.S. Cheung M.L. Maguire T.J. Stevens R.W. Broadhurst DANGLE: a Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure J. Magn. Reson. 202 2010 223 233
-
(2010)
J. Magn. Reson.
, vol.202
, pp. 223-233
-
-
Cheung, M.S.1
Maguire, M.L.2
Stevens, T.J.3
Broadhurst, R.W.4
-
34
-
-
84859567766
-
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
-
J. Lehtivarjo K. Tuppurainen T. Hassinen R. Laatikainen M. Peräkylä Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction J. Biomol. NMR 52 2012 257 267
-
(2012)
J. Biomol. NMR
, vol.52
, pp. 257-267
-
-
Lehtivarjo, J.1
Tuppurainen, K.2
Hassinen, T.3
Laatikainen, R.4
Peräkylä, M.5
-
37
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
S.A. Adcock J.A. McCammon Molecular dynamics: survey of methods for simulating the activity of proteins Chem. Rev. 106 2006 1589 1615
-
(2006)
Chem. Rev.
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
38
-
-
33845553743
-
Model-Free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
-
G. Lipari A. Szabo Model-Free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results J. Am. Chem. Soc. 104 1982 4559 4570
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 4559-4570
-
-
Lipari, G.1
Szabo, A.2
-
39
-
-
33646719091
-
Model-Free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of Validity
-
G. Lipari A. Szabo Model-Free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of Validity J. Am. Chem. Soc. 104 1982 4546 4559
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
40
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
C. Dominguez R. Boelens A.M. Bonvin HADDOCK: a protein-protein docking approach based on biochemical or biophysical information J. Am. Chem. Soc. 125 2003 1731 1737
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
41
-
-
77955391393
-
The HADDOCK web server for data-driven biomolecular docking
-
S.J. de Vries M. van Dijk A.M. Bonvin The HADDOCK web server for data-driven biomolecular docking Nat. Protoc. 5 2010 883 897
-
(2010)
Nat. Protoc.
, vol.5
, pp. 883-897
-
-
De Vries, S.J.1
Van Dijk, M.2
Bonvin, A.M.3
-
42
-
-
0004014257
-
-
Department of Biochemistry and Molecular Biology, University Collage London
-
S.J. Hubbard J.M. Thornton NACCESS 1993 Department of Biochemistry and Molecular Biology, University Collage London
-
(1993)
NACCESS
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
43
-
-
0030587774
-
Zif268 protein-DNA complex refined at 1.6 A: A model system for understanding zinc finger-DNA interactions
-
M. Elrod-Erickson M.A. Rould L. Nekludova C.O. Pabo Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions Structure 4 1996 1171 1180
-
(1996)
Structure
, vol.4
, pp. 1171-1180
-
-
Elrod-Erickson, M.1
Rould, M.A.2
Nekludova, L.3
Pabo, C.O.4
-
44
-
-
84879343421
-
2 zinc fingers from eubacterial ros homologs
-
2 zinc fingers from eubacterial ros homologs Mol. Biol. Evol. 30 2013 1504 1513
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 1504-1513
-
-
Netti, F.1
Malgieri, G.2
Esposito, S.3
Palmieri, M.4
Baglivo, I.5
Isernia, C.6
Omichinski, J.G.7
Pedone, P.V.8
Lartillot, N.9
Fattorusso, R.10
-
45
-
-
84875797582
-
Structural Zn(II) implies a switch from fully cooperative to partly downhill folding in highly homologous proteins
-
M. Palmieri G. Malgieri L. Russo I. Baglivo S. Esposito F. Netti A. Del Gatto I. de Paola L. Zaccaro P.V. Pedone C. Isernia D. Milardi R. Fattorusso Structural Zn(II) implies a switch from fully cooperative to partly downhill folding in highly homologous proteins J. Am. Chem. Soc. 135 2013 5220 5228
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 5220-5228
-
-
Palmieri, M.1
Malgieri, G.2
Russo, L.3
Baglivo, I.4
Esposito, S.5
Netti, F.6
Del Gatto, A.7
De Paola, I.8
Zaccaro, L.9
Pedone, P.V.10
Isernia, C.11
Milardi, D.12
Fattorusso, R.13
-
46
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, Load-Balanced, and Scalable molecular simulation
-
B. Hess C. Kutzner D. van der Spoel E. Lindahl GROMACS 4: algorithms for highly efficient, Load-Balanced, and Scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
47
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
V. Hornak R. Abel A. Okur B. Strockbine A. Roitberg C. Simmerling Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 65 2006 712 725
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
52
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
R. Koradi M. Billeter K. Wüthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph 14 1996 29 32
-
(1996)
J. Mol. Graph
, vol.14
, pp. 29-32
-
-
Koradi, R.1
Billeter, M.2
Wüthrich, K.3
-
54
-
-
34547592557
-
MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
-
I.W. Davis A. Leaver-Fay V.B. Chen J.N. Block G.J. Kapral X. Wang L.W. Murray W.B. Arendall J. Snoeyink J.S. Richardson D.C. Richardson MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 375-W383
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
Wang, X.6
Murray, L.W.7
Arendall, W.B.8
Snoeyink, J.9
Richardson, J.S.10
Richardson, D.C.11
-
55
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
W. Kabsch C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
56
-
-
0032528033
-
Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
-
G. Cornilescu J.L. Marquardt M. Ottiger A. Bax Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase J. Am. Chem. Soc. 120 1998 6836 6837
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 6836-6837
-
-
Cornilescu, G.1
Marquardt, J.L.2
Ottiger, M.3
Bax, A.4
-
57
-
-
33846803179
-
DISPLAR: An accurate method for predicting DNA-binding sites on protein surfaces
-
H. Tjong H.X. Zhou DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces Nucleic Acids Res. 35 2007 1465 1477
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 1465-1477
-
-
Tjong, H.1
Zhou, H.X.2
-
58
-
-
67849110013
-
3D-DART: A DNA structure modelling server
-
M. van Dijk A.M. Bonvin 3D-DART: a DNA structure modelling server Nucleic Acids Res. 37 2009 W235 W239
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 235-W239
-
-
Van Dijk, M.1
Bonvin, A.M.2
-
59
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
X.J. Lu W.K. Olson 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Res. 31 2003 5108 5121
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
|