-
1
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.W. Hung, G.J. Kapral, and R.W. Grosse-Kunstleve PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkóczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
-
3
-
-
84908221627
-
Modelling dynamics in protein crystal structures by ensemble refinement
-
B.T. Burnley, P.V. Afonine, P.D. Adams, and P. Gros Modelling dynamics in protein crystal structures by ensemble refinement eLife 1 2012 e00311
-
(2012)
ELife
, vol.1
, pp. 00311
-
-
Burnley, B.T.1
Afonine, P.V.2
Adams, P.D.3
Gros, P.4
-
4
-
-
70350509577
-
KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
-
V.B. Chen, I.W. Davis, and D.C. Richardson KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program Protein Science 18 2009 2403 2409
-
(2009)
Protein Science
, vol.18
, pp. 2403-2409
-
-
Chen, V.B.1
Davis, I.W.2
Richardson, D.C.3
-
5
-
-
74549178560
-
MolProbity: All-atom structure validation for macromolecular crystallography
-
V.B. Chen, W.B. Arendall, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr 66 Pt 1 2010 12 21
-
(2010)
Acta Crystallogr
, vol.66
, Issue.PART 1
, pp. 12-21
-
-
Chen, V.B.1
Arendall, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
-
6
-
-
0017187836
-
The nature of the accessible and buried surfaces in proteins
-
C. Chothia The nature of the accessible and buried surfaces in proteins J. Mol. Biol. 105 1976 1 12
-
(1976)
J. Mol. Biol.
, vol.105
, pp. 1-12
-
-
Chothia, C.1
-
7
-
-
0000920828
-
The packing of alpha-helices - Simple coiled-coils
-
F.H.C. Crick The packing of alpha-helices - simple coiled-coils Acta Crystallogr. 6 1953 689 697
-
(1953)
Acta Crystallogr.
, vol.6
, pp. 689-697
-
-
Crick, F.H.C.1
-
8
-
-
32044456003
-
The backrub motion: How protein backbone shrugs when a sidechain dances
-
I.W. Davis, W.B. Arendall 3rd, D.C. Richardson, and J.S. Richardson The backrub motion: how protein backbone shrugs when a sidechain dances Structure 14 2006 265 274
-
(2006)
Structure
, vol.14
, pp. 265-274
-
-
Davis, I.W.1
Arendall, W.B.2
Richardson, D.C.3
Richardson, J.S.4
-
9
-
-
0019522383
-
Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution
-
J. Deisenhofer Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution Biochemistry 20 1981 2361 2370
-
(1981)
Biochemistry
, vol.20
, pp. 2361-2370
-
-
Deisenhofer, J.1
-
10
-
-
2342525085
-
Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography
-
M.A. DePristo, P.I. de Bakker, and T.L. Blundell Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography Structure 12 2004 831 838
-
(2004)
Structure
, vol.12
, pp. 831-838
-
-
Depristo, M.A.1
De Bakker, P.I.2
Blundell, T.L.3
-
12
-
-
23144441604
-
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures
-
J.F. Doreleijers, A.J. Nederveen, W. Vranken, J. Lin, A.M. Bonvin, R. Kaptein, J.L. Markley, and E.L. Ulrich BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures J. Biomol. NMR 32 2005 1 12
-
(2005)
J. Biomol. NMR
, vol.32
, pp. 1-12
-
-
Doreleijers, J.F.1
Nederveen, A.J.2
Vranken, W.3
Lin, J.4
Bonvin, A.M.5
Kaptein, R.6
Markley, J.L.7
Ulrich, E.L.8
-
14
-
-
80053626537
-
Accessing protein conformational ensembles using room-temperature X-ray crystallography
-
J.S. Fraser, H. van den Bedem, A.J. Samelson, P.T. Lang, J.M. Holton, N. Echols, and T. Alber Accessing protein conformational ensembles using room-temperature X-ray crystallography Proc. Natl. Acad. Sci. USA 108 2011 16247 16252
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 16247-16252
-
-
Fraser, J.S.1
Van Den Bedem, H.2
Samelson, A.J.3
Lang, P.T.4
Holton, J.M.5
Echols, N.6
Alber, T.7
-
15
-
-
4043059295
-
Staphylococcus aureus protein A induces airway epithelial inflammatory responses by activating TNFR1
-
M.I. Gómez, A. Lee, B. Reddy, A. Muir, G. Soong, A. Pitt, A. Cheung, and A. Prince Staphylococcus aureus protein A induces airway epithelial inflammatory responses by activating TNFR1 Nat. Med. 10 2004 842 848
-
(2004)
Nat. Med.
, vol.10
, pp. 842-848
-
-
Gómez, M.I.1
Lee, A.2
Reddy, B.3
Muir, A.4
Soong, G.5
Pitt, A.6
Cheung, A.7
Prince, A.8
-
16
-
-
0026801084
-
Three-dimensional solution structure of the B domain of staphylococcal protein A: Comparisons of the solution and crystal structures
-
H. Gouda, H. Torigoe, A. Saito, M. Sato, Y. Arata, and I. Shimada Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures Biochemistry 31 1992 9665 9672
-
(1992)
Biochemistry
, vol.31
, pp. 9665-9672
-
-
Gouda, H.1
Torigoe, H.2
Saito, A.3
Sato, M.4
Arata, Y.5
Shimada, I.6
-
17
-
-
0032488629
-
NMR study of the interaction between the B domain of staphylococcal protein A and the Fc portion of immunoglobulin G
-
H. Gouda, M. Shiraishi, H. Takahashi, K. Kato, H. Torigoe, Y. Arata, and I. Shimada NMR study of the interaction between the B domain of staphylococcal protein A and the Fc portion of immunoglobulin G Biochemistry 37 1998 129 136
-
(1998)
Biochemistry
, vol.37
, pp. 129-136
-
-
Gouda, H.1
Shiraishi, M.2
Takahashi, H.3
Kato, K.4
Torigoe, H.5
Arata, Y.6
Shimada, I.7
-
18
-
-
0034625113
-
Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity
-
M. Graille, E.A. Stura, A.L. Corper, B.J. Sutton, M.J. Taussig, J.B. Charbonnier, and G.J. Silverman Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity Proc. Natl. Acad. Sci. USA 97 2000 5399 5404
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5399-5404
-
-
Graille, M.1
Stura, E.A.2
Corper, A.L.3
Sutton, B.J.4
Taussig, M.J.5
Charbonnier, J.B.6
Silverman, G.J.7
-
19
-
-
0034665906
-
Protein A is the von Willebrand factor binding protein on Staphylococcus aureus
-
J. Hartleib, N. Köhler, R.B. Dickinson, G.S. Chhatwal, J.J. Sixma, O.M. Hartford, T.J. Foster, G. Peters, B.E. Kehrel, and M. Herrmann Protein A is the von Willebrand factor binding protein on Staphylococcus aureus Blood 96 2000 2149 2156
-
(2000)
Blood
, vol.96
, pp. 2149-2156
-
-
Hartleib, J.1
Köhler, N.2
Dickinson, R.B.3
Chhatwal, G.S.4
Sixma, J.J.5
Hartford, O.M.6
Foster, T.J.7
Peters, G.8
Kehrel, B.E.9
Herrmann, M.10
-
20
-
-
0031884383
-
All individual domains of staphylococcal protein A show Fab binding
-
B. Jansson, M. Uhlén, and P.A. Nygren All individual domains of staphylococcal protein A show Fab binding FEMS Immunol. Med. Microbiol. 20 1998 69 78
-
(1998)
FEMS Immunol. Med. Microbiol.
, vol.20
, pp. 69-78
-
-
Jansson, B.1
Uhlén, M.2
Nygren, P.A.3
-
21
-
-
0029330511
-
Kinetic analysis of the interaction between protein A domain variants and human Fc using plasmon resonance detection
-
L. Jendeberg, B. Persson, R. Andersson, R. Karlsson, M. Uhlén, and B. Nilsson Kinetic analysis of the interaction between protein A domain variants and human Fc using plasmon resonance detection J. Mol. Recognit. 8 1995 270 278
-
(1995)
J. Mol. Recognit.
, vol.8
, pp. 270-278
-
-
Jendeberg, L.1
Persson, B.2
Andersson, R.3
Karlsson, R.4
Uhlén, M.5
Nilsson, B.6
-
22
-
-
0030043942
-
The mechanism of binding staphylococcal protein A to immunoglobin G does not involve helix unwinding
-
L. Jendeberg, M. Tashiro, R. Tejero, B.A. Lyons, M. Uhlén, G.T. Montelione, and B. Nilsson The mechanism of binding staphylococcal protein A to immunoglobin G does not involve helix unwinding Biochemistry 35 1996 22 31
-
(1996)
Biochemistry
, vol.35
, pp. 22-31
-
-
Jendeberg, L.1
Tashiro, M.2
Tejero, R.3
Lyons, B.A.4
Uhlén, M.5
Montelione, G.T.6
Nilsson, B.7
-
23
-
-
20944434880
-
Cryo-cooling in macromolecular crystallography: Advantages, disadvantages and optimization
-
D.H. Juers, and B.W. Matthews Cryo-cooling in macromolecular crystallography: advantages, disadvantages and optimization Q. Rev. Biophys. 37 2004 105 119
-
(2004)
Q. Rev. Biophys.
, vol.37
, pp. 105-119
-
-
Juers, D.H.1
Matthews, B.W.2
-
24
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
O.F. Lange, N.A. Lakomek, C. Farès, G.F. Schröder, K.F. Walter, S. Becker, J. Meiler, H. Grubmüller, C. Griesinger, and B.L. de Groot Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution Science 320 2008 1471 1475
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.A.2
Farès, C.3
Schröder, G.F.4
Walter, K.F.5
Becker, S.6
Meiler, J.7
Grubmüller, H.8
Griesinger, C.9
De Groot, B.L.10
-
25
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
K. Lindorff-Larsen, R.B. Best, M.A. Depristo, C.M. Dobson, and M. Vendruscolo Simultaneous determination of protein structure and dynamics Nature 433 2005 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
-
26
-
-
34447508216
-
Phaser crystallographic software
-
A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Cryst. 40 2007 658 674
-
(2007)
J. Appl. Cryst.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
27
-
-
0037094114
-
An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation
-
G. Minasov, X. Wang, and B.K. Shoichet An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation J. Am. Chem. Soc. 124 2002 5333 5340
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5333-5340
-
-
Minasov, G.1
Wang, X.2
Shoichet, B.K.3
-
28
-
-
0035005366
-
Preorganized secondary structure as an important determinant of fast protein folding
-
J.K. Myers, and T.G. Oas Preorganized secondary structure as an important determinant of fast protein folding Nat. Struct. Biol. 8 2001 552 558
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 552-558
-
-
Myers, J.K.1
Oas, T.G.2
-
29
-
-
0034104817
-
Staphylococcus aureus protein A recognizes platelet gC1qR/p33: A novel mechanism for staphylococcal interactions with platelets
-
T. Nguyen, B. Ghebrehiwet, and E.I. Peerschke Staphylococcus aureus protein A recognizes platelet gC1qR/p33: a novel mechanism for staphylococcal interactions with platelets Infect. Immun. 68 2000 2061 2068
-
(2000)
Infect. Immun.
, vol.68
, pp. 2061-2068
-
-
Nguyen, T.1
Ghebrehiwet, B.2
Peerschke, E.I.3
-
30
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
31
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
32
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices
-
J.S. Richardson, and D.C. Richardson Amino acid preferences for specific locations at the ends of alpha helices Science 240 1988 1648 1652
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
33
-
-
0013033189
-
Mage, probe, and kinemages. Chapter 25.2.8
-
M.G. Rossman, E. Arnold, Kluwer Academic Publishers Dordrecht, the Netherlands
-
D.C. Richardson, and J.S. Richardson MAGE, PROBE, and Kinemages. Chapter 25.2.8 M.G. Rossman, E. Arnold, International Tables for Crystallography Vol. F 2001 Kluwer Academic Publishers Dordrecht, the Netherlands 727 730
-
(2001)
International Tables for Crystallography
, vol.F
, pp. 727-730
-
-
Richardson, D.C.1
Richardson, J.S.2
-
34
-
-
0026638608
-
Sorting of protein A to the staphylococcal cell wall
-
O. Schneewind, P. Model, and V.A. Fischetti Sorting of protein A to the staphylococcal cell wall Cell 70 1992 267 281
-
(1992)
Cell
, vol.70
, pp. 267-281
-
-
Schneewind, O.1
Model, P.2
Fischetti, V.A.3
-
35
-
-
77950793231
-
Experimental phasing with SHELXC/D/E: Combining chain tracing with density modification
-
G.M. Sheldrick Experimental phasing with SHELXC/D/E: combining chain tracing with density modification Acta Crystallogr. D Biol. Crystallogr. 66 2010 479 485
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 479-485
-
-
Sheldrick, G.M.1
-
36
-
-
0033783032
-
Receptor binding and membrane fusion in virus entry: The influenza hemagglutinin
-
J.J. Skehel, and D.C. Wiley Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin Annu. Rev. Biochem. 69 2000 531 569
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 531-569
-
-
Skehel, J.J.1
Wiley, D.C.2
-
37
-
-
0029906640
-
Solution structure of the E-domain of staphylococcal protein A
-
M.A. Starovasnik, N.J. Skelton, M.P. O'Connell, R.F. Kelley, D. Reilly, and W.J. Fairbrother Solution structure of the E-domain of staphylococcal protein A Biochemistry 35 1996 15558 15569
-
(1996)
Biochemistry
, vol.35
, pp. 15558-15569
-
-
Starovasnik, M.A.1
Skelton, N.J.2
O'Connell, M.P.3
Kelley, R.F.4
Reilly, D.5
Fairbrother, W.J.6
-
38
-
-
0031551582
-
High-resolution solution NMR structure of the Z domain of staphylococcal protein A
-
M. Tashiro, R. Tejero, D.E. Zimmerman, B. Celda, B. Nilsson, and G.T. Montelione High-resolution solution NMR structure of the Z domain of staphylococcal protein A J. Mol. Biol. 272 1997 573 590
-
(1997)
J. Mol. Biol.
, vol.272
, pp. 573-590
-
-
Tashiro, M.1
Tejero, R.2
Zimmerman, D.E.3
Celda, B.4
Nilsson, B.5
Montelione, G.T.6
-
39
-
-
34247495231
-
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
-
T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, P.D. Adams, N.W. Moriarty, P. Zwart, R.J. Read, D. Turk, and L.W. Hung Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models Acta Crystallogr. D Biol. Crystallogr. 63 2007 597 610
-
(2007)
Acta Crystallogr. D Biol. Crystallogr.
, vol.63
, pp. 597-610
-
-
Terwilliger, T.C.1
Grosse-Kunstleve, R.W.2
Afonine, P.V.3
Adams, P.D.4
Moriarty, N.W.5
Zwart, P.6
Read, R.J.7
Turk, D.8
Hung, L.W.9
-
40
-
-
37349103121
-
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
-
T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.H. Zwart, L.W. Hung, R.J. Read, and P.D. Adams Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Acta Crystallogr. D Biol. Crystallogr. 64 2008 61 69
-
(2008)
Acta Crystallogr. D Biol. Crystallogr.
, vol.64
, pp. 61-69
-
-
Terwilliger, T.C.1
Grosse-Kunstleve, R.W.2
Afonine, P.V.3
Moriarty, N.W.4
Zwart, P.H.5
Hung, L.W.6
Read, R.J.7
Adams, P.D.8
-
41
-
-
0025196843
-
Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: Structural changes between the free B domain in solution and the Fc-bound B domain in crystal
-
H. Torigoe, I. Shimada, A. Saito, M. Sato, and Y. Arata Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: structural changes between the free B domain in solution and the Fc-bound B domain in crystal Biochemistry 29 1990 8787 8793
-
(1990)
Biochemistry
, vol.29
, pp. 8787-8793
-
-
Torigoe, H.1
Shimada, I.2
Saito, A.3
Sato, M.4
Arata, Y.5
-
43
-
-
84883403423
-
Automated identification of functional dynamic contact networks from X-ray crystallography
-
H. van den Bedem, G. Bhabha, K. Yang, P.E. Wright, and J.S. Fraser Automated identification of functional dynamic contact networks from X-ray crystallography Nat. Methods 10 2013 896 902
-
(2013)
Nat. Methods
, vol.10
, pp. 896-902
-
-
Van Den Bedem, H.1
Bhabha, G.2
Yang, K.3
Wright, P.E.4
Fraser, J.S.5
-
44
-
-
0034257929
-
The 1.0 A crystal structure of Ca(2+)-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
-
M.A. Wilson, and A.T. Brunger The 1.0 A crystal structure of Ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity J. Mol. Biol. 301 2000 1237 1256
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 1237-1256
-
-
Wilson, M.A.1
Brunger, A.T.2
-
45
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: Small-probe contact dots with explicit hydrogen atoms
-
J.M. Word, S.C. Lovell, T.H. LaBean, H.C. Taylor, M.E. Zalis, B.K. Presley, J.S. Richardson, and D.C. Richardson Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms J. Mol. Biol. 285 1999 1711 1733
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1711-1733
-
-
Word, J.M.1
Lovell, S.C.2
Labean, T.H.3
Taylor, H.C.4
Zalis, M.E.5
Presley, B.K.6
Richardson, J.S.7
Richardson, D.C.8
-
46
-
-
1642493921
-
Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data
-
D. Zheng, J.M. Aramini, and G.T. Montelione Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data Protein Sci. 13 2004 549 554
-
(2004)
Protein Sci.
, vol.13
, pp. 549-554
-
-
Zheng, D.1
Aramini, J.M.2
Montelione, G.T.3
|