-
1
-
-
36749088906
-
Determining the architectures of macromolecular assemblies
-
Alber F., Dokudovskaya S., Veenhoff L.M., Zhang W., Kipper J., Devos D., Suprapto A., Karni-Schmidt O., Williams R., Chait B.T., et al. Determining the architectures of macromolecular assemblies. Nature 450 (2007) 683-694
-
(2007)
Nature
, vol.450
, pp. 683-694
-
-
Alber, F.1
Dokudovskaya, S.2
Veenhoff, L.M.3
Zhang, W.4
Kipper, J.5
Devos, D.6
Suprapto, A.7
Karni-Schmidt, O.8
Williams, R.9
Chait, B.T.10
-
2
-
-
0032489015
-
The cell as a collection of protein machines - preparing the next generation of biologists
-
Alberts B. The cell as a collection of protein machines - preparing the next generation of biologists. Cell 92 (1998) 291-294
-
(1998)
Cell
, vol.92
, pp. 291-294
-
-
Alberts, B.1
-
3
-
-
33845204189
-
Stability and dynamics of virus capsids described by coarse-grained modeling
-
Arkhipov A., Freddolino P.L., and Schulten K. Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 14 (2006) 1767-1777
-
(2006)
Structure
, vol.14
, pp. 1767-1777
-
-
Arkhipov, A.1
Freddolino, P.L.2
Schulten, K.3
-
4
-
-
48749137581
-
Stochastic boundary conditions for molecular dynamics simulations of ST2 water
-
Brünger A.T., Brooks III C.L., and Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105 (1984) 495-498
-
(1984)
Chem. Phys. Lett.
, vol.105
, pp. 495-498
-
-
Brünger, A.T.1
Brooks III, C.L.2
Karplus, M.3
-
5
-
-
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. A 51 (1995) 69-80
-
(1995)
Acta Crystallogr. A
, vol.51
, pp. 69-80
-
-
Chapman, M.S.1
-
6
-
-
0035783170
-
Real space refinement of acto-myosin structures from sectioned muscle
-
Chen L.F., Blanc E., Chapman M.S., and Taylor K.A. Real space refinement of acto-myosin structures from sectioned muscle. J. Struct. Biol. 133 (2001) 221-232
-
(2001)
J. Struct. Biol.
, vol.133
, pp. 221-232
-
-
Chen, L.F.1
Blanc, E.2
Chapman, M.S.3
Taylor, K.A.4
-
7
-
-
0037374820
-
Ni-Zn-[Fe-S] and Ni-Ni-[Fe-S] clusters in closed and open α subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase
-
Darnault C., Volbeda A., Kim E.J., Legrand P., Vernède X., Lindahl P.A., and Fontecilla-Camps J.C. Ni-Zn-[Fe-S] and Ni-Ni-[Fe-S] clusters in closed and open α subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nat. Struct. Biol. 10 (2003) 271-279
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 271-279
-
-
Darnault, C.1
Volbeda, A.2
Kim, E.J.3
Legrand, P.4
Vernède, X.5
Lindahl, P.A.6
Fontecilla-Camps, J.C.7
-
8
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe N., and MacKerrell Jr. A.D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21 (2000) 86-104
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerrell Jr., A.D.2
-
9
-
-
0036089703
-
Single-particle imaging of macromolecules by cryo-electron microscopy
-
Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 309-319
-
(2002)
Annu. Rev. Biophys. Biomol. Struct.
, vol.31
, pp. 309-319
-
-
Frank, J.1
-
10
-
-
0037319733
-
Electron microscopy of functional ribosome complexes
-
Frank J. Electron microscopy of functional ribosome complexes. Biopolymers 68 (2003) 223-233
-
(2003)
Biopolymers
, vol.68
, pp. 223-233
-
-
Frank, J.1
-
12
-
-
33845346092
-
The ribosome and the mechanism of protein synthesis
-
Frank J., and Spahn C.M.T. The ribosome and the mechanism of protein synthesis. Rep. Prog. Phys. 69 (2006) 1383-1417
-
(2006)
Rep. Prog. Phys.
, vol.69
, pp. 1383-1417
-
-
Frank, J.1
Spahn, C.M.T.2
-
14
-
-
0038275890
-
Study of the structural dynamics of the E. coli 70S ribosome using real space refinement
-
Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., et al. Study of the structural dynamics of the E. coli 70S ribosome using real space refinement. Cell 113 (2003) 789-801
-
(2003)
Cell
, vol.113
, pp. 789-801
-
-
Gao, H.1
Sengupta, J.2
Valle, M.3
Korostelev, A.4
Eswar, N.5
Stagg, S.M.6
Van Roey, P.7
Agrawal, R.K.8
Harvey, S.C.9
Sali, A.10
-
16
-
-
0035312645
-
Steered molecular dynamics and mechanical functions of proteins
-
Isralewitz B., Gao M., and Schulten K. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11 (2001) 224-230
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 224-230
-
-
Isralewitz, B.1
Gao, M.2
Schulten, K.3
-
18
-
-
41449099769
-
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
-
Jolley C.C., Wells S.A., Fromme P., and Thorpe M.F. Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. Biophys. J. 94 (2008) 1613-1621
-
(2008)
Biophys. J.
, vol.94
, pp. 1613-1621
-
-
Jolley, C.C.1
Wells, S.A.2
Fromme, P.3
Thorpe, M.F.4
-
19
-
-
0032300804
-
Conserved geometrical base-pairing patters in RNA
-
Leontis N.B., and Westhof E. Conserved geometrical base-pairing patters in RNA. Q. Rev. Biophys. 31 (1998) 399-455
-
(1998)
Q. Rev. Biophys.
, vol.31
, pp. 399-455
-
-
Leontis, N.B.1
Westhof, E.2
-
20
-
-
36749079267
-
Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data
-
Li W., and Frank J. Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data. Proc. Natl. Acad. Sci. USA 104 (2007) 16540-16545
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 16540-16545
-
-
Li, W.1
Frank, J.2
-
21
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell Jr. A., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J., Field M.J., Fischer S., Gao J., Guo H., Ha S., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
22
-
-
33646495214
-
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps
-
Mitra K., and Frank J. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 299-317
-
(2006)
Annu. Rev. Biophys. Biomol. Struct.
, vol.35
, pp. 299-317
-
-
Mitra, K.1
Frank, J.2
-
23
-
-
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 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, C.L.6
Ban, N.7
Frank, J.8
-
24
-
-
33646524478
-
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements
-
Mitra K., Schaffitzel C., Fabiola F., Chapman M., Ban N., and Frank J. Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Mol. Cell 22 (2006) 533-543
-
(2006)
Mol. Cell
, vol.22
, pp. 533-543
-
-
Mitra, K.1
Schaffitzel, C.2
Fabiola, F.3
Chapman, M.4
Ban, N.5
Frank, J.6
-
25
-
-
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., and Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 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
-
26
-
-
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
-
27
-
-
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
-
28
-
-
0033776856
-
Macromolecular structure determination by cryo-electron microscopy
-
Saibil H.R. Macromolecular structure determination by cryo-electron microscopy. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 1215-1222
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 1215-1222
-
-
Saibil, H.R.1
-
29
-
-
0037435031
-
From words to literature in structural proteomics
-
Sali A., Glaeser R., Earnest T., and Baumeister W. From words to literature in structural proteomics. Nature 422 (2003) 216-225
-
(2003)
Nature
, vol.422
, pp. 216-225
-
-
Sali, A.1
Glaeser, R.2
Earnest, T.3
Baumeister, W.4
-
30
-
-
36749078686
-
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
-
Schröder G.F., Brunger A.T., and Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 15 (2007) 1630-1641
-
(2007)
Structure
, vol.15
, pp. 1630-1641
-
-
Schröder, G.F.1
Brunger, A.T.2
Levitt, M.3
-
31
-
-
27644491082
-
Structures of the bacterial ribosome at 3.5 Å resolution
-
Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Cate J.H.D. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310 (2005) 827-834
-
(2005)
Science
, vol.310
, pp. 827-834
-
-
Schuwirth, B.S.1
Borovinskaya, M.A.2
Hau, C.W.3
Zhang, W.4
Vila-Sanjurjo, A.5
Holton, J.M.6
Cate, J.H.D.7
-
32
-
-
33749354360
-
Structure of the 70S ribosome complexed with mRNA and tRNA
-
Selmer M., Dunham C.M., Murphy IV F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
-
(2006)
Science
, vol.313
, pp. 1935-1942
-
-
Selmer, M.1
Dunham, C.M.2
Murphy IV, F.V.3
Weixlbaumer, A.4
Petry, S.5
Kelley, A.C.6
Weir, J.R.7
Ramakrishnan, V.8
-
33
-
-
33847193915
-
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
-
Shih A.Y., Freddolino P.L., Arkhipov A., and Schulten K. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. J. Struct. Biol. 157 (2007) 579-592
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 579-592
-
-
Shih, A.Y.1
Freddolino, P.L.2
Arkhipov, A.3
Schulten, K.4
-
34
-
-
34249930159
-
Single-molecule experiments in vitro and in silico
-
Sotomayor M., and Schulten K. Single-molecule experiments in vitro and in silico. Science 316 (2007) 1144-1148
-
(2007)
Science
, vol.316
, pp. 1144-1148
-
-
Sotomayor, M.1
Schulten, K.2
-
35
-
-
0027184774
-
Difference imaging of adenovirus: Bridging the resolution gap between X-ray crystallography and electron microscopy
-
Stewart P.L., Fuller S.D., and Burnett R.M. Difference imaging of adenovirus: Bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO J. 12 (1993) 2589-2599
-
(1993)
EMBO J.
, vol.12
, pp. 2589-2599
-
-
Stewart, P.L.1
Fuller, S.D.2
Burnett, R.M.3
-
36
-
-
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
-
37
-
-
4344716056
-
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
-
Tama F., Miyashita O., and Brooks III C.L. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147 (2004) 315-326
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 315-326
-
-
Tama, F.1
Miyashita, O.2
Brooks III, C.L.3
-
38
-
-
33645075435
-
Refinement of protein structures by iterative comparative modeling and cryoEM density fitting
-
Topf M., Baker M.L., Marc-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
Marc-Renom, M.A.3
Chiu, W.4
Sali, A.5
-
39
-
-
38949092920
-
Protein structure fitting and refinement guided by cryo-EM density
-
Topf M., Lasker K., Webb B., Wolfson H., Chiu W., and Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 16 (2008) 295-307
-
(2008)
Structure
, vol.16
, pp. 295-307
-
-
Topf, M.1
Lasker, K.2
Webb, B.3
Wolfson, H.4
Chiu, W.5
Sali, A.6
-
40
-
-
0242407184
-
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy
-
Valle M., Zavialov A., Li W., Stagg S.M., Sengupta J., Nielsen R.C., Nissen P., Harvey S.C., Ehrenberg M., and Frank J. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10 (2003) 899-906
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 899-906
-
-
Valle, M.1
Zavialov, A.2
Li, W.3
Stagg, S.M.4
Sengupta, J.5
Nielsen, R.C.6
Nissen, P.7
Harvey, S.C.8
Ehrenberg, M.9
Frank, J.10
-
41
-
-
33745813129
-
Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies
-
Velazquez-Muriel J.A., Valle M., Santamaría-Pang A., Kakadiaris I.A., and Carazo J.M. Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies. Structure 14 (2006) 1115-1126
-
(2006)
Structure
, vol.14
, pp. 1115-1126
-
-
Velazquez-Muriel, J.A.1
Valle, M.2
Santamaría-Pang, A.3
Kakadiaris, I.A.4
Carazo, J.M.5
-
42
-
-
0033669710
-
Evidence for cleft closure in actomyosin upon ADP release
-
Volkmann N., Hanein D., Ouyang G., Trybus K.M., DeRosier D.J., and Lowey S. Evidence for cleft closure in actomyosin upon ADP release. Nat. Struct. Biol. 7 (2000) 1147-1155
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 1147-1155
-
-
Volkmann, N.1
Hanein, D.2
Ouyang, G.3
Trybus, K.M.4
DeRosier, D.J.5
Lowey, S.6
-
43
-
-
34848830419
-
Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics
-
Wells D.B., Abramkina V., and Aksimentiev A. Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics. J. Chem. Phys. 127 (2007) 125101-125110
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 125101-125110
-
-
Wells, D.B.1
Abramkina, V.2
Aksimentiev, A.3
-
44
-
-
0035783173
-
Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data
-
Wriggers W., and Birmanns S. Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data. J. Struct. Biol. 133 (2001) 193-202
-
(2001)
J. Struct. Biol.
, vol.133
, pp. 193-202
-
-
Wriggers, W.1
Birmanns, S.2
-
45
-
-
0034802465
-
Modeling tricks and fitting techniques for multiresolution structures
-
Wriggers W., and Chacón P. Modeling tricks and fitting techniques for multiresolution structures. Structure 9 (2001) 779-788
-
(2001)
Structure
, vol.9
, pp. 779-788
-
-
Wriggers, W.1
Chacón, P.2
-
46
-
-
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
-
47
-
-
0033863336
-
Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures
-
Wriggers W., Agrawal R.K., Drew D.L., McCammon A., and Frank J. Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures. Biophys. J. 79 (2000) 1670-1678
-
(2000)
Biophys. J.
, vol.79
, pp. 1670-1678
-
-
Wriggers, W.1
Agrawal, R.K.2
Drew, D.L.3
McCammon, A.4
Frank, J.5
-
48
-
-
0043123152
-
Tools for the automatic identification and classification of RNA base pairs
-
Yang H., Jossinet F., Leontis N., Chen L., Westbrook J., Berman H., and Westhof E. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31 (2003) 3450-3460
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3450-3460
-
-
Yang, H.1
Jossinet, F.2
Leontis, N.3
Chen, L.4
Westbrook, J.5
Berman, H.6
Westhof, E.7
-
49
-
-
0037764042
-
Molecular dynamics simulations of peptides and proteins with amplified collective motions
-
Zhang Z., Shi Y., and Liu H. Molecular dynamics simulations of peptides and proteins with amplified collective motions. Biophys. J. 84 (2003) 3583-3593
-
(2003)
Biophys. J.
, vol.84
, pp. 3583-3593
-
-
Zhang, Z.1
Shi, Y.2
Liu, H.3
-
50
-
-
0035783362
-
Automated identification of filaments in cryoelectron microscopy images
-
Zhu Y., Carrangher B., Kriegman D.J., Milligan R.A., and Potter C.S. Automated identification of filaments in cryoelectron microscopy images. J. Struct. Biol. 135 (2001) 302-312
-
(2001)
J. Struct. Biol.
, vol.135
, pp. 302-312
-
-
Zhu, Y.1
Carrangher, B.2
Kriegman, D.J.3
Milligan, R.A.4
Potter, C.S.5
|