-
1
-
-
0032511137
-
Multiple open forms of ribose-binding protein trace the path of its conformational change
-
Bjorkman A.J., and Mowbray S.L. Multiple open forms of ribose-binding protein trace the path of its conformational change. J. Mol. Biol. 279 (1998) 651-664
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 651-664
-
-
Bjorkman, A.J.1
Mowbray, S.L.2
-
2
-
-
0027945890
-
Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis
-
Bjorkman A.J., Binnie R.A., Zhang H., Cole L.B., Hermodson M.A., and Mowbray S.L. Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis. J. Biol. Chem. 269 (1994) 30206-30211
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 30206-30211
-
-
Bjorkman, A.J.1
Binnie, R.A.2
Zhang, H.3
Cole, L.B.4
Hermodson, M.A.5
Mowbray, S.L.6
-
3
-
-
0026597444
-
The free R value: a novel statistical quantity for assessing the accuracy of crystal structures
-
Brunger A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472-474
-
(1992)
Nature
, vol.355
, pp. 472-474
-
-
Brunger, A.T.1
-
4
-
-
0001897686
-
Assessment of phase accuracy by cross validation: the free R value. Methods and applications
-
Brunger A.T. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr. D Biol. Crystallogr. 49 (1993) 24-36
-
(1993)
Acta Crystallogr. D Biol. Crystallogr.
, vol.49
, pp. 24-36
-
-
Brunger, A.T.1
-
5
-
-
13844296499
-
Low-resolution crystallography is coming of age
-
Brunger A.T. Low-resolution crystallography is coming of age. Structure 13 (2005) 171-172
-
(2005)
Structure
, vol.13
, pp. 171-172
-
-
Brunger, A.T.1
-
6
-
-
0023140814
-
Crystallographic R factor refinement by molecular dynamics
-
Brunger A.T., Kuriyan J., and Karplus M. Crystallographic R factor refinement by molecular dynamics. Science 235 (1987) 458-460
-
(1987)
Science
, vol.235
, pp. 458-460
-
-
Brunger, A.T.1
Kuriyan, J.2
Karplus, M.3
-
7
-
-
3543012707
-
Crystallography and NMR system (CNS): a new software system 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., Nilges N., Pannu N.S., Read R.J., et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
-
(1998)
Acta Crystallogr. 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
Nilges, N.8
Pannu, N.S.9
Read, R.J.10
-
8
-
-
1942521664
-
Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization
-
Ceulemans H., and Russell R.B. Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. J. Mol. Biol. 338 (2004) 783-793
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 783-793
-
-
Ceulemans, H.1
Russell, R.B.2
-
9
-
-
0036297629
-
Multi-resolution contour-based fitting of macromolecular structures
-
Chacon P., and Wriggers W. Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 317 (2002) 375-384
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 375-384
-
-
Chacon, P.1
Wriggers, W.2
-
10
-
-
0001832403
-
Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function
-
Chapman M.S. Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr. A51 (1995) 69-80
-
(1995)
Acta Crystallogr.
, vol.A51
, pp. 69-80
-
-
Chapman, M.S.1
-
13
-
-
33746414364
-
Considerations for the refinement of low resolution crystal structures
-
DeLaBarre B., and Brunger A.T. Considerations for the refinement of low resolution crystal structures. Acta Crystallogr. D Biol. Crystallogr. 26 (2006) 923-932
-
(2006)
Acta Crystallogr. D Biol. Crystallogr.
, vol.26
, pp. 923-932
-
-
DeLaBarre, B.1
Brunger, A.T.2
-
14
-
-
2342518038
-
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
-
Delarue M., and Dumas P. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl. Acad. Sci. USA 101 (2004) 6957-6962
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6957-6962
-
-
Delarue, M.1
Dumas, P.2
-
15
-
-
0000307306
-
On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor
-
Diamond R. On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor. Acta Crystallogr. A 46 (1990) 425-435
-
(1990)
Acta Crystallogr. A
, vol.46
, pp. 425-435
-
-
Diamond, R.1
-
16
-
-
33846408714
-
EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies
-
Dror O., Lasker K., Nussinov R., and Wolfson H. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. Acta Crystallogr. D Biol. Crystallogr. 63 (2007) 42-49
-
(2007)
Acta Crystallogr. D Biol. Crystallogr.
, vol.63
, pp. 42-49
-
-
Dror, O.1
Lasker, K.2
Nussinov, R.3
Wolfson, H.4
-
17
-
-
14844311200
-
Fitting of high-resolution structures into electron microscopy reconstruction images
-
Fabiola F., and Chapman M.S. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure 13 (2005) 389-400
-
(2005)
Structure
, vol.13
, pp. 389-400
-
-
Fabiola, F.1
Chapman, M.S.2
-
18
-
-
19844377583
-
The 13 structure of a chaperonin GroEL protein substrate complex by cryo-electron microscopy
-
Falke S., Tama F., Brooks III C.L., Gogol E.P., and Fisher M.T. The 13 structure of a chaperonin GroEL protein substrate complex by cryo-electron microscopy. J. Mol. Biol. 348 (2005) 219-223
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 219-223
-
-
Falke, S.1
Tama, F.2
Brooks III, C.L.3
Gogol, E.P.4
Fisher, M.T.5
-
19
-
-
14844303319
-
Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement
-
Gao H., and Frank J. Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement. Structure 13 (2005) 401-406
-
(2005)
Structure
, vol.13
, pp. 401-406
-
-
Gao, H.1
Frank, J.2
-
21
-
-
0030931612
-
Prediction of protein conformational freedom from distance constraints
-
de Groot B.L., van Aalten D.M.F., Scheek R.M., Amadei A., Vriend G., and Berendsen H.J.C. Prediction of protein conformational freedom from distance constraints. Proteins Struct. Funct. Genet. 29 (1997) 240-251
-
(1997)
Proteins Struct. Funct. Genet.
, vol.29
, pp. 240-251
-
-
de Groot, B.L.1
van Aalten, D.M.F.2
Scheek, R.M.3
Amadei, A.4
Vriend, G.5
Berendsen, H.J.C.6
-
22
-
-
0032006209
-
Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme
-
Hayward S., and Berendsen H.J.C. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 30 (1998) 144-154
-
(1998)
Proteins
, vol.30
, pp. 144-154
-
-
Hayward, S.1
Berendsen, H.J.C.2
-
23
-
-
17044432465
-
Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase
-
Hinsen K., Reuter N., Navaza J., Stokes D.L., and Lacapère J.-J. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys. J. 88 (2005) 818-827
-
(2005)
Biophys. J.
, vol.88
, pp. 818-827
-
-
Hinsen, K.1
Reuter, N.2
Navaza, J.3
Stokes, D.L.4
Lacapère, J.-J.5
-
24
-
-
84918314491
-
Refinement of large structures by simultaneous minimization of energy and R factor
-
Jack A., and Levitt M. Refinement of large structures by simultaneous minimization of energy and R factor. Acta Crystallogr. A34 (1978) 931-935
-
(1978)
Acta Crystallogr.
, vol.A34
, pp. 931-935
-
-
Jack, A.1
Levitt, M.2
-
25
-
-
0025294520
-
Refinement of protein dynamic structure: normal mode refinement
-
Kidera A., and Go N. Refinement of protein dynamic structure: normal mode refinement. Proc. Natl. Acad. Sci. USA 87 (1990) 3718-3722
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 3718-3722
-
-
Kidera, A.1
Go, N.2
-
27
-
-
27844444793
-
Structure of the E. coli protein-conducting channel bound to a translating ribosome
-
Mitra K., Schaffitzel C., Shaikh T., Tama F., Jenni S., Brooks III C.L., Ban N., and Frank J. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438 (2005) 318-324
-
(2005)
Nature
, vol.438
, pp. 318-324
-
-
Mitra, K.1
Schaffitzel, C.2
Shaikh, T.3
Tama, F.4
Jenni, S.5
Brooks III, C.L.6
Ban, N.7
Frank, J.8
-
28
-
-
34249944597
-
Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution
-
Poon B.K., Chen X., Lu M., Vyas N.K., Quiocho F.A., Wang Q., and Ma J. Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution. Proc. Natl. Acad. Sci. USA 104 (2007) 7869-7874
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 7869-7874
-
-
Poon, B.K.1
Chen, X.2
Lu, M.3
Vyas, N.K.4
Quiocho, F.A.5
Wang, Q.6
Ma, J.7
-
29
-
-
0344120722
-
Fast 3D motif search of EM density maps using a locally normalized cross-correlation function
-
Rath B.K., Hegerl R., Leith A., Shaikh T.R., Wagenknecht T., and Frank J. Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol. 144 (2003) 95-103
-
(2003)
J. Struct. Biol.
, vol.144
, pp. 95-103
-
-
Rath, B.K.1
Hegerl, R.2
Leith, A.3
Shaikh, T.R.4
Wagenknecht, T.5
Frank, J.6
-
30
-
-
26844527626
-
High-order analytic translation matrix elements for real-space six-dimensional polar Fourier correlations
-
Ritchie D.W. High-order analytic translation matrix elements for real-space six-dimensional polar Fourier correlations. J. Appl. Crystallogr. 38 (2005) 808-818
-
(2005)
J. Appl. Crystallogr.
, vol.38
, pp. 808-818
-
-
Ritchie, D.W.1
-
31
-
-
0033776245
-
Docking structures of domains into maps from cryo-electron microscopy using local correlation
-
Roseman A.M. Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 1332-1340
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 1332-1340
-
-
Roseman, A.M.1
-
32
-
-
0033780164
-
Fitting atomic models into electron-microscopy maps
-
Rossmann M.G. Fitting atomic models into electron-microscopy maps. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 1341-1349
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 1341-1349
-
-
Rossmann, M.G.1
-
33
-
-
14844338484
-
Combining X-ray crystallography and electron microscopy
-
Rossmann M.G., Morais M.C., Leiman P.G., and Zhang W. Combining X-ray crystallography and electron microscopy. Structure 13 (2005) 355-362
-
(2005)
Structure
, vol.13
, pp. 355-362
-
-
Rossmann, M.G.1
Morais, M.C.2
Leiman, P.G.3
Zhang, W.4
-
34
-
-
3242883858
-
On the potential of normal-mode analysis for solving difficult molecular-replacement problems
-
Suhre K., and Sanejouand Y.-H. On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 796-799
-
(2004)
Acta Crystallogr. D Biol. Crystallogr.
, vol.60
, pp. 796-799
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
35
-
-
33748351384
-
NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
-
Suhre K., Navaza J., and Sanejouand Y.-H. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr. D Biol. Crystallogr. 62 (2006) 1098-1100
-
(2006)
Acta Crystallogr. D Biol. Crystallogr.
, vol.62
, pp. 1098-1100
-
-
Suhre, K.1
Navaza, J.2
Sanejouand, Y.-H.3
-
36
-
-
1642355235
-
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
-
Tama F., Miyashita O., and Brooks III C.L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337 (2004) 985-999
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 985-999
-
-
Tama, F.1
Miyashita, O.2
Brooks III, C.L.3
-
37
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77 (1996) 1905-1908
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
38
-
-
33645075435
-
Refinement of protein structures by iterative comparative modeling and cryoEM density fitting
-
Topf M., Baker M.L., Marti-Renom M.A., Chiu W., and Sali A. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J. Mol. Biol. 357 (2006) 1655-1668
-
(2006)
J. Mol. Biol.
, vol.357
, pp. 1655-1668
-
-
Topf, M.1
Baker, M.L.2
Marti-Renom, M.A.3
Chiu, W.4
Sali, A.5
-
39
-
-
0032779888
-
Quantitative fitting of atomic models into observed densities derived by electron microscopy
-
Volkmann N., and Hanein D. Quantitative fitting of atomic models into observed densities derived by electron microscopy. J. Struct. Biol. 125 (1999) 176-184
-
(1999)
J. Struct. Biol.
, vol.125
, pp. 176-184
-
-
Volkmann, N.1
Hanein, D.2
-
40
-
-
0032780181
-
Situs: a package for docking crystal structures into low-resolution maps from electron microscopy
-
Wriggers W., Milligan R.A., and McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125 (1999) 185-195
-
(1999)
J. Struct. Biol.
, vol.125
, pp. 185-195
-
-
Wriggers, W.1
Milligan, R.A.2
McCammon, J.A.3
-
41
-
-
0742306445
-
Topology representing neural networks reconcile biomolecular shape, structure, and dynamics
-
Wriggers W., Chacon P., Kovacs J.A., Tama F., and Birmanns S. Topology representing neural networks reconcile biomolecular shape, structure, and dynamics. Neurocomputing 56 (2004) 365-379
-
(2004)
Neurocomputing
, vol.56
, pp. 365-379
-
-
Wriggers, W.1
Chacon, P.2
Kovacs, J.A.3
Tama, F.4
Birmanns, S.5
-
42
-
-
0037285752
-
A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy
-
Wu X., Milne J.L., Borgnia M.J., Rostapshov A.V., Subramaniam S., and Brooks B.R. A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J. Struct. Biol. 141 (2003) 63-76
-
(2003)
J. Struct. Biol.
, vol.141
, pp. 63-76
-
-
Wu, X.1
Milne, J.L.2
Borgnia, M.J.3
Rostapshov, A.V.4
Subramaniam, S.5
Brooks, B.R.6
|