-
1
-
-
76449098262
-
PHENIX: a comprehensive Python-based system for macromolecular structure solution
-
Adams P.D., Afonine P.V., Bunkoczi G., Chen V.B., Davis I.W., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta. Crystallogr. D Biol. Crystallogr. 2010, 66:213-221.
-
(2010)
Acta. Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkoczi, G.3
Chen, V.B.4
Davis, I.W.5
-
2
-
-
48749103296
-
Integrating diverse data for structure determination of macromolecular assemblies
-
Alber F., Forster F., Korkin D., Topf M., Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem. 2008, 77:443-477.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 443-477
-
-
Alber, F.1
Forster, F.2
Korkin, D.3
Topf, M.4
Sali, A.5
-
3
-
-
77957585573
-
Cryo-EM of macromolecular assemblies at near-atomic resolution
-
Baker M.L., Zhang J., Ludtke S.J., Chiu W. Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat. Protoc. 2010, 5:1697-1708.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 1697-1708
-
-
Baker, M.L.1
Zhang, J.2
Ludtke, S.J.3
Chiu, W.4
-
4
-
-
0026597444
-
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
-
Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992, 355:472-475.
-
(1992)
Nature
, vol.355
, pp. 472-475
-
-
Brünger, A.T.1
-
5
-
-
3543012707
-
Crystallography and NMR system: a new software system for macromolecular structure determination
-
Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., et al. Crystallography and NMR system: a new software system for macromolecular structure determination. Acta Crystallogr. 1998, D54:905-921.
-
(1998)
Acta Crystallogr.
, vol.D54
, pp. 905-921
-
-
Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
-
6
-
-
0012791435
-
On the theory of filter amplifiers
-
Butterworth S. On the theory of filter amplifiers. Wireless Engineer 1930, 7:536-541.
-
(1930)
Wireless Engineer
, vol.7
, pp. 536-541
-
-
Butterworth, S.1
-
8
-
-
77950684778
-
Adeno-associated virus and AAV vectors for gene delivery
-
CRC Press, Boca Raton, N.S. Templeton (Ed.)
-
Carter B.J., Peluso R.W., Burstein H. Adeno-associated virus and AAV vectors for gene delivery. Gene and Cell Therapy: Therapeutic Mechanisms and Strategies 2008, 115-156. CRC Press, Boca Raton. N.S. Templeton (Ed.).
-
(2008)
Gene and Cell Therapy: Therapeutic Mechanisms and Strategies
, pp. 115-156
-
-
Carter, B.J.1
Peluso, R.W.2
Burstein, H.3
-
9
-
-
84862896208
-
Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method
-
Chan K.-Y., Trabuco L.G., Schreiner E., Schulten K. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. Biopolymers 2012, 97:678-686.
-
(2012)
Biopolymers
, vol.97
, pp. 678-686
-
-
Chan, K.-Y.1
Trabuco, L.G.2
Schreiner, E.3
Schulten, K.4
-
10
-
-
80052442678
-
Symmetry-restrained flexible fitting for symmetric EM maps
-
Chan K.-Y., Gumbart J., McGreevy R., Watermeyer J., Sewell B.T., Schulten K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure 2011, 19:1211-1218.
-
(2011)
Structure
, vol.19
, pp. 1211-1218
-
-
Chan, K.-Y.1
Gumbart, J.2
McGreevy, R.3
Watermeyer, J.4
Sewell, B.T.5
Schulten, K.6
-
11
-
-
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. 1995, A51:69-80.
-
(1995)
Acta Crystallogr.
, vol.A51
, pp. 69-80
-
-
Chapman, M.S.1
-
12
-
-
0035783170
-
Real space refinement of acto-myosin structures from sectioned muscle
-
Chen L.F., Blanc E., Chapman M.S., Taylor K.A. Real space refinement of acto-myosin structures from sectioned muscle. J. Struct. Biol. 2001, 133:221-232.
-
(2001)
J. Struct. Biol.
, vol.133
, pp. 221-232
-
-
Chen, L.F.1
Blanc, E.2
Chapman, M.S.3
Taylor, K.A.4
-
14
-
-
0000651098
-
A real-space refinement procedure for proteins
-
Diamond R. A real-space refinement procedure for proteins. Acta Crystallogr. 1971, A27:436-452.
-
(1971)
Acta Crystallogr.
, vol.A27
, pp. 436-452
-
-
Diamond, R.1
-
15
-
-
84864003612
-
Structural insight into the unique properties of adeno-associated virus serotype 9
-
Dimattia M.A., Nam H.J., Van Vliet K., Mitchell M., Bennett A., et al. Structural insight into the unique properties of adeno-associated virus serotype 9. J. Virol. 2012, 86:6947-6958.
-
(2012)
J. Virol.
, vol.86
, pp. 6947-6958
-
-
Dimattia, M.A.1
Nam, H.J.2
Van Vliet, K.3
Mitchell, M.4
Bennett, A.5
-
16
-
-
77949535720
-
Features and development of Coot
-
Emsley P., Lohkamp B., Scott W.G., Cowtan K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 2010, 66:486-501.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
17
-
-
38049034590
-
Protein structure modeling with modeller
-
John Wiley & Sons, Inc., Suppl. 15, A.D. Baxevanis (Ed.)
-
Eswar N., Eramian D., Webb B., Shen M., Sali A. Protein structure modeling with modeller. Current Protocols in Bioinformatics 2006, 5.6.10-5.6.30. John Wiley & Sons, Inc., Suppl. 15. A.D. Baxevanis (Ed.).
-
(2006)
Current Protocols in Bioinformatics
-
-
Eswar, N.1
Eramian, D.2
Webb, B.3
Shen, M.4
Sali, A.5
-
18
-
-
14844311200
-
Fitting of high-resolution structures into electron microscopy reconstruction images
-
Fabiola F., Chapman M.S. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure (Camb) 2005, 13:389-400.
-
(2005)
Structure (Camb)
, vol.13
, pp. 389-400
-
-
Fabiola, F.1
Chapman, M.S.2
-
19
-
-
51549084591
-
Sharpening high resolution information in single particle electron cryomicroscopy
-
Fernandez J.J., Luque D., Caston J.R., Carrascosa J.L. Sharpening high resolution information in single particle electron cryomicroscopy. J. Struct. Biol. 2008, 164:170-175.
-
(2008)
J. Struct. Biol.
, vol.164
, pp. 170-175
-
-
Fernandez, J.J.1
Luque, D.2
Caston, J.R.3
Carrascosa, J.L.4
-
20
-
-
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., et al. Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell 2003, 113:789-801.
-
(2003)
Cell
, vol.113
, pp. 789-801
-
-
Gao, H.1
Sengupta, J.2
Valle, M.3
Korostelev, A.4
Eswar, N.5
-
22
-
-
33751210120
-
Structurally mapping the diverse phenotype of adeno-associated virus serotype 4
-
Govindasamy L., Padron E., McKenna R., Muzyczka N., Kaludov N., et al. Structurally mapping the diverse phenotype of adeno-associated virus serotype 4. J. Virol. 2006, 80:11556-11570.
-
(2006)
J. Virol.
, vol.80
, pp. 11556-11570
-
-
Govindasamy, L.1
Padron, E.2
McKenna, R.3
Muzyczka, N.4
Kaludov, N.5
-
23
-
-
0033777020
-
Resolution measurement in structures derived from single particles
-
Grigorieff N. Resolution measurement in structures derived from single particles. Acta Crystallogr. D Biol. Crystallogr. 2000, 56:1270-1277.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 1270-1277
-
-
Grigorieff, N.1
-
24
-
-
33845348200
-
FREALIGN: high-resolution refinement of single particle structures
-
Grigorieff N. FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol. 2007, 157:117-125.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 117-125
-
-
Grigorieff, N.1
-
25
-
-
79953108462
-
Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy
-
Grigorieff N., Harrison S.C. Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr. Opin Struct. Biol. 2011, 21:265-273.
-
(2011)
Curr. Opin Struct. Biol.
, vol.21
, pp. 265-273
-
-
Grigorieff, N.1
Harrison, S.C.2
-
26
-
-
44949131860
-
In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses
-
Grimm D., Lee J.S., Wang L., Desai T., Akache B., et al. In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses. J Virol 2008, 82:5887-5911.
-
(2008)
J Virol
, vol.82
, pp. 5887-5911
-
-
Grimm, D.1
Lee, J.S.2
Wang, L.3
Desai, T.4
Akache, B.5
-
27
-
-
77953748314
-
-
Torsion Angle Refinement and Dynamics as a Tool to Aid Crystallographic Structure Determination, Proceedings of the ASME 2009 Internation Design Engineering Conferences & Computers and Information in Engineering Conferences, San Diego, Vol. DETC2009
-
Grosse-Kunstleve, R.W., Moriarty, N.W., Adams, P.D. 2009. Torsion Angle Refinement and Dynamics as a Tool to Aid Crystallographic Structure Determination, Proceedings of the ASME 2009 Internation Design Engineering Conferences & Computers and Information in Engineering Conferences, San Diego, Vol. DETC2009, p. 87737.
-
(2009)
, pp. 87737
-
-
Grosse-Kunstleve, R.W.1
Moriarty, N.W.2
Adams, P.D.3
-
28
-
-
33845336533
-
Bsoft: image processing and molecular modeling for electron microscopy
-
Heymann J.B., Belnap D.M. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 2007, 157:3-18.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 3-18
-
-
Heymann, J.B.1
Belnap, D.M.2
-
29
-
-
0348014440
-
TEXTAL system: artificial intelligence techniques for automated protein model building
-
Ioerger T.R., Sacchettini J.C. TEXTAL system: artificial intelligence techniques for automated protein model building. Methods Enzymol. 2003, 374:244-270.
-
(2003)
Methods Enzymol.
, vol.374
, pp. 244-270
-
-
Ioerger, T.R.1
Sacchettini, J.C.2
-
30
-
-
0030501416
-
A pseudo-cell based approach to efficient crystallographic refinement of viruses
-
Jacobson D.H., Hogle J.M., Filman D.J. A pseudo-cell based approach to efficient crystallographic refinement of viruses. Acta Crystallogr. 1996, D52:693-711.
-
(1996)
Acta Crystallogr.
, vol.D52
, pp. 693-711
-
-
Jacobson, D.H.1
Hogle, J.M.2
Filman, D.J.3
-
31
-
-
23744500479
-
-
Jones, E., Oliphant, T., Peterson, P., et. al. 2001. SciPy: open source scientific tools for Python, http://www.scipy.org/.
-
(2001)
SciPy: open source scientific tools for Python
-
-
Jones, E.1
Oliphant, T.2
Peterson, P.3
-
32
-
-
0002701773
-
Crystallographic refinement of macromolecules having non-crystallographic symmetry
-
Jones T.A., Liljas L. Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Crystallogr. 1984, A40:50-57.
-
(1984)
Acta Crystallogr.
, vol.A40
, pp. 50-57
-
-
Jones, T.A.1
Liljas, L.2
-
33
-
-
54849391500
-
DNA shuffling of adeno-associated virus yields functionally diverse viral progeny
-
Koerber J.T., Jang J.H., Schaffer D.V. DNA shuffling of adeno-associated virus yields functionally diverse viral progeny. Mol. Ther. 2008, 16:1703-1709.
-
(2008)
Mol. Ther.
, vol.16
, pp. 1703-1709
-
-
Koerber, J.T.1
Jang, J.H.2
Schaffer, D.V.3
-
34
-
-
60649103238
-
Appion: an integrated, database-driven pipeline to facilitate EM image processing
-
Lander G.C., Stagg S.M., Voss N.R., Cheng A., Fellmann D., et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 2009, 166:95-102.
-
(2009)
J. Struct. Biol.
, vol.166
, pp. 95-102
-
-
Lander, G.C.1
Stagg, S.M.2
Voss, N.R.3
Cheng, A.4
Fellmann, D.5
-
35
-
-
77957947549
-
Determining macromolecular assembly structures by molecular docking and fitting into an electron density map
-
Lasker K., Sali A., Wolfson H.J. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins 2010, 78:3205-3211.
-
(2010)
Proteins
, vol.78
, pp. 3205-3211
-
-
Lasker, K.1
Sali, A.2
Wolfson, H.J.3
-
36
-
-
63449125993
-
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly
-
Lasker K., Topf M., Sali A., Wolfson H.J. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J. Mol. Biol. 2009, 388:180-194.
-
(2009)
J. Mol. Biol.
, vol.388
, pp. 180-194
-
-
Lasker, K.1
Topf, M.2
Sali, A.3
Wolfson, H.J.4
-
37
-
-
84864829908
-
Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5å resolution
-
Lerch Thomas.F., O'Donnell Jason.K., Meyer Nancy.L., Xie Q., Taylor Kenneth.A., et al. Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5å resolution. Structure 2012, 20:1310-1320.
-
(2012)
Structure
, vol.20
, pp. 1310-1320
-
-
Lerch, T.1
O'Donnell, J.2
Meyer, N.3
Xie, Q.4
Taylor, K.5
-
38
-
-
30344450073
-
Mutations on the external surfaces of adeno-associated virus type 2 capsids that affect transduction and neutralization
-
Lochrie M.A., Tatsuno G.P., Christie B., McDonnell J.W., Zhou S., et al. Mutations on the external surfaces of adeno-associated virus type 2 capsids that affect transduction and neutralization. J. Virol. 2006, 80:821-834.
-
(2006)
J. Virol.
, vol.80
, pp. 821-834
-
-
Lochrie, M.A.1
Tatsuno, G.P.2
Christie, B.3
McDonnell, J.W.4
Zhou, S.5
-
39
-
-
84862903714
-
The 2010 cryo-em modeling challenge
-
Ludtke S.J., Lawson C.L., Kleywegt G.J., Berman H., Chiu W. The 2010 cryo-em modeling challenge. Biopolymers 2012, 97:651-654.
-
(2012)
Biopolymers
, vol.97
, pp. 651-654
-
-
Ludtke, S.J.1
Lawson, C.L.2
Kleywegt, G.J.3
Berman, H.4
Chiu, W.5
-
40
-
-
32344438754
-
Directed evolution of adeno-associated virus yields enhanced gene delivery vectors
-
Maheshri N., Koerber J.T., Kaspar B.K., Schaffer D.V. Directed evolution of adeno-associated virus yields enhanced gene delivery vectors. Nat. Biotechnol. 2006, 24:198-204.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 198-204
-
-
Maheshri, N.1
Koerber, J.T.2
Kaspar, B.K.3
Schaffer, D.V.4
-
41
-
-
20144378098
-
ACE: automated CTF estimation
-
Mallick S.P., Carragher B., Potter C.S., Kriegman D.J. ACE: automated CTF estimation. Ultramicroscopy 2005, 104:8-29.
-
(2005)
Ultramicroscopy
, vol.104
, pp. 8-29
-
-
Mallick, S.P.1
Carragher, B.2
Potter, C.S.3
Kriegman, D.J.4
-
42
-
-
33644820684
-
Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response
-
Manno C.S., Pierce G.F., Arruda V.R., Glader B., Ragni M., et al. Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response. Nat. Med. 2006, 12:342-347.
-
(2006)
Nat. Med.
, vol.12
, pp. 342-347
-
-
Manno, C.S.1
Pierce, G.F.2
Arruda, V.R.3
Glader, B.4
Ragni, M.5
-
43
-
-
33846131680
-
-
O'Reilly, Beijing, Sebastopol, CA
-
Martelli A. Python in a Nutshell 2006, O'Reilly, Beijing, Sebastopol, CA. 2nd ed.
-
(2006)
Python in a Nutshell
-
-
Martelli, A.1
-
44
-
-
84862329652
-
Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20
-
McCraw D.M., O'Donnell J.K., Taylor K.A., Stagg S.M., Chapman M.S. Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. Virology 2012, 431:40-49.
-
(2012)
Virology
, vol.431
, pp. 40-49
-
-
McCraw, D.M.1
O'Donnell, J.K.2
Taylor, K.A.3
Stagg, S.M.4
Chapman, M.S.5
-
45
-
-
33646524478
-
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements
-
Mitra K., Schaffitzel C., Fabiola F., Chapman M.S., Ban N., et al. Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Mol. Cell 2006, 22:533-543.
-
(2006)
Mol. Cell
, vol.22
, pp. 533-543
-
-
Mitra, K.1
Schaffitzel, C.2
Fabiola, F.3
Chapman, M.S.4
Ban, N.5
-
46
-
-
0001142644
-
Parvoviridae: the viruses and their replication
-
Lippincott Williams & Wilkins, Philadelphia, B.N. Fields (Ed.)
-
Muzyczka N., Berns K.I. Parvoviridae: the viruses and their replication. Virology 2001, 2327-2360. Lippincott Williams & Wilkins, Philadelphia. B.N. Fields (Ed.).
-
(2001)
Virology
, pp. 2327-2360
-
-
Muzyczka, N.1
Berns, K.I.2
-
47
-
-
36049020398
-
Structure of adeno-associated virus serotype 8, a gene therapy vector
-
Nam H.J., Lane M.D., Padron E., Gurda B., McKenna R., et al. Structure of adeno-associated virus serotype 8, a gene therapy vector. J. Virol. 2007, 81:12260-12271.
-
(2007)
J. Virol.
, vol.81
, pp. 12260-12271
-
-
Nam, H.J.1
Lane, M.D.2
Padron, E.3
Gurda, B.4
McKenna, R.5
-
48
-
-
0036795476
-
On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation
-
Navaza J., Lepault J., Rey F.A., Alvarez-Rua C., Borge J. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta Crystallogr. D Biol. Crystallogr. 2002, 58:1820-1825.
-
(2002)
Acta Crystallogr. D Biol. Crystallogr.
, vol.58
, pp. 1820-1825
-
-
Navaza, J.1
Lepault, J.2
Rey, F.A.3
Alvarez-Rua, C.4
Borge, J.5
-
49
-
-
79251598995
-
A new clustering of antibody CDR loop conformations
-
North B., Lehmann A., Dunbrack R.L. A new clustering of antibody CDR loop conformations. J. Mol. Biol. 2011, 406:228-256.
-
(2011)
J. Mol. Biol.
, vol.406
, pp. 228-256
-
-
North, B.1
Lehmann, A.2
Dunbrack, R.L.3
-
50
-
-
84875028639
-
-
Guide to NumPy.
-
Oliphant, T., 2006. Guide to NumPy.
-
(2006)
-
-
Oliphant, T.1
-
51
-
-
77956256437
-
Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle
-
Pereira J.H., Ralston C.Y., Douglas N.R., Meyer D., Knee K.M., et al. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J. Biol. Chem. 2010, 285:27958-27966.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 27958-27966
-
-
Pereira, J.H.1
Ralston, C.Y.2
Douglas, N.R.3
Meyer, D.4
Knee, K.M.5
-
52
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26:1781-1802.
-
(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
-
53
-
-
0028070557
-
Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement
-
Rice L.M., Brünger A.T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 1994, 19:277-290.
-
(1994)
Proteins
, vol.19
, pp. 277-290
-
-
Rice, L.M.1
Brünger, A.T.2
-
54
-
-
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. 2000, 56:1332-1340.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr.
, vol.56
, pp. 1332-1340
-
-
Roseman, A.M.1
-
55
-
-
33544454902
-
-
Kluwer Academic Publishers., Dortrecht, Netherlands
-
Rossmann M.G., Arnold E. Crystallography of Biological Molecules, International Tables for Crystallography 2001, Kluwer Academic Publishers., Dortrecht, Netherlands.
-
(2001)
Crystallography of Biological Molecules, International Tables for Crystallography
-
-
Rossmann, M.G.1
Arnold, E.2
-
56
-
-
0035783056
-
Combining electron microscopic with x-ray crystallographic structures
-
Rossmann M.G., Bernal R., Pletnev S.V. Combining electron microscopic with x-ray crystallographic structures. J. Struct. Biol. 2001, 136:190-200.
-
(2001)
J. Struct. Biol.
, vol.136
, pp. 190-200
-
-
Rossmann, M.G.1
Bernal, R.2
Pletnev, S.V.3
-
57
-
-
0035782663
-
Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination
-
Saad A., Ludtke S.J., Jakana J., Rixon F.J., Tsuruta H., et al. Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 2001, 133:32-42.
-
(2001)
J. Struct. Biol.
, vol.133
, pp. 32-42
-
-
Saad, A.1
Ludtke, S.J.2
Jakana, J.3
Rixon, F.J.4
Tsuruta, H.5
-
58
-
-
77951623055
-
Super-resolution biomolecular crystallography with low-resolution data
-
Schröder G.F., Levitt M., Brunger A.T. Super-resolution biomolecular crystallography with low-resolution data. Nature 2010, 464:1218-1222.
-
(2010)
Nature
, vol.464
, pp. 1218-1222
-
-
Schröder, G.F.1
Levitt, M.2
Brunger, A.T.3
-
59
-
-
58049204808
-
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs
-
Shaikh T.R., Gao H., Baxter W.T., Asturias F.J., Boisset N., et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat. Protoc. 2008, 3:1941-1974.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1941-1974
-
-
Shaikh, T.R.1
Gao, H.2
Baxter, W.T.3
Asturias, F.J.4
Boisset, N.5
-
60
-
-
35548955563
-
Characterization of the relationship of AAV capsid domain swapping to liver transduction efficiency
-
Shen X., Storm T., Kay M.A. Characterization of the relationship of AAV capsid domain swapping to liver transduction efficiency. Mol. Ther. 2007, 15:1955-1962.
-
(2007)
Mol. Ther.
, vol.15
, pp. 1955-1962
-
-
Shen, X.1
Storm, T.2
Kay, M.A.3
-
62
-
-
20544468931
-
Automated molecular microscopy: the new leginon system
-
Suloway C., Pulokas J., Fellmann D., Cheng A., Guerra F., et al. Automated molecular microscopy: the new leginon system. J. Struct. Biol. 2005, 151:41-60.
-
(2005)
J. Struct. Biol.
, vol.151
, pp. 41-60
-
-
Suloway, C.1
Pulokas, J.2
Fellmann, D.3
Cheng, A.4
Guerra, F.5
-
63
-
-
4344716056
-
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
-
Tama F., Miyashita O., Brooks C.L. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 2004, 147:315-326.
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 315-326
-
-
Tama, F.1
Miyashita, O.2
Brooks, C.L.3
-
64
-
-
33845332754
-
EMAN2: An extensible image processing suite for electron microscopy
-
Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., et al. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 2007, 157:38-46.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 38-46
-
-
Tang, G.1
Peng, L.2
Baldwin, P.R.3
Mann, D.S.4
Jiang, W.5
-
65
-
-
0000496875
-
Crystallographic fast Fourier transforms
-
Ten Eyck L.F. Crystallographic fast Fourier transforms. Acta Crystallogr. 1973, A29:183-191.
-
(1973)
Acta Crystallogr.
, vol.A29
, pp. 183-191
-
-
Ten Eyck, L.F.1
-
66
-
-
38949092920
-
Protein structure fitting and refinement guided by Cryo-EM density
-
Topf M., Lasker K., Webb B., Wolfson H., Chiu W., et al. Protein structure fitting and refinement guided by Cryo-EM density. Structure 2008, 16:295-307.
-
(2008)
Structure
, vol.16
, pp. 295-307
-
-
Topf, M.1
Lasker, K.2
Webb, B.3
Wolfson, H.4
Chiu, W.5
-
67
-
-
42949089487
-
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
-
Trabuco L.G., Villa E., Mitra K., Frank J., Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 2008, 16:673-683.
-
(2008)
Structure
, vol.16
, pp. 673-683
-
-
Trabuco, L.G.1
Villa, E.2
Mitra, K.3
Frank, J.4
Schulten, K.5
-
68
-
-
79954417945
-
Scoring functions for cryoEM density fitting
-
Vasishtan D., Topf M. Scoring functions for cryoEM density fitting. J. Struct. Biol. 2011, 174:333-343.
-
(2011)
J. Struct. Biol.
, vol.174
, pp. 333-343
-
-
Vasishtan, D.1
Topf, M.2
-
69
-
-
68149170539
-
Confidence intervals for fitting of atomic models into low-resolution densities
-
Volkmann N. Confidence intervals for fitting of atomic models into low-resolution densities. Acta Crystallogr. D Biol. Crystallogr. 2009, 65:679-689.
-
(2009)
Acta Crystallogr. D Biol. Crystallogr.
, vol.65
, pp. 679-689
-
-
Volkmann, N.1
-
70
-
-
0032779888
-
Quantitative fitting of atomic models into observed densities derived by electron microscopy [published erratum appears in J Struct Biol 1999 Dec 15;128(2):223]
-
Volkmann N., Hanein D. Quantitative fitting of atomic models into observed densities derived by electron microscopy [published erratum appears in J Struct Biol 1999 Dec 15;128(2):223]. J. Struct. Biol. 1999, 125:176-184.
-
(1999)
J. Struct. Biol.
, vol.125
, pp. 176-184
-
-
Volkmann, N.1
Hanein, D.2
-
71
-
-
1842562409
-
Structure of adeno-associated virus serotype 5
-
Walters R.W., Agbandje-McKenna M., Bowman V.D., Moninger T.O., Olson N.H., et al. Structure of adeno-associated virus serotype 5. J. Virol. 2004, 78:3361-3371.
-
(2004)
J. Virol.
, vol.78
, pp. 3361-3371
-
-
Walters, R.W.1
Agbandje-McKenna, M.2
Bowman, V.D.3
Moninger, T.O.4
Olson, N.H.5
-
72
-
-
80052496589
-
Impact of pre-existing immunity on gene transfer to nonhuman primate liver with adeno-associated virus 8 vectors
-
Wang L., Calcedo R., Bell P., Lin J., Grant R.L., et al. Impact of pre-existing immunity on gene transfer to nonhuman primate liver with adeno-associated virus 8 vectors. Hum. Gene. Ther. 2011, 22:1389-1401.
-
(2011)
Hum. Gene. Ther.
, vol.22
, pp. 1389-1401
-
-
Wang, L.1
Calcedo, R.2
Bell, P.3
Lin, J.4
Grant, R.L.5
-
73
-
-
84862863609
-
Real-space refinement with DireX: From global fitting to side-chain improvements
-
Wang Z., Schröder G.F. Real-space refinement with DireX: From global fitting to side-chain improvements. Biopolymers 2012, 97:687-697.
-
(2012)
Biopolymers
, vol.97
, pp. 687-697
-
-
Wang, Z.1
Schröder, G.F.2
-
74
-
-
0033808531
-
Monoclonal antibodies against the adeno-associated virus type 2 (AAV-2) capsid: epitope mapping and identification of capsid domains involved in AAV-2-cell interaction and neutralization of AAV-2 infection
-
Wobus C.E., Hugle-Dorr B., Girod A., Petersen G., Hallek M., et al. Monoclonal antibodies against the adeno-associated virus type 2 (AAV-2) capsid: epitope mapping and identification of capsid domains involved in AAV-2-cell interaction and neutralization of AAV-2 infection. J. Virol. 2000, 74:9281-9293.
-
(2000)
J. Virol.
, vol.74
, pp. 9281-9293
-
-
Wobus, C.E.1
Hugle-Dorr, B.2
Girod, A.3
Petersen, G.4
Hallek, M.5
-
75
-
-
77955358961
-
Using Situs for the integration of multi-resolution structures
-
Wriggers W. Using Situs for the integration of multi-resolution structures. Biophys. Rev. 2010, 2:21-27.
-
(2010)
Biophys. Rev.
, vol.2
, pp. 21-27
-
-
Wriggers, W.1
-
76
-
-
0036678455
-
The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy
-
Xie Q., Bu W., Bhatia S., Hare J., Somasundaram T., et al. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy. Proc. Natl. Acad. Sci. USA 2002, 99:10405-10410.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 10405-10410
-
-
Xie, Q.1
Bu, W.2
Bhatia, S.3
Hare, J.4
Somasundaram, T.5
-
77
-
-
0345414561
-
Issues of resolution and polymorphism in single-particle reconstruction
-
Yang S., Yu X., Galkin V.E., Egelman E.H. Issues of resolution and polymorphism in single-particle reconstruction. J. Struct. Biol. 2003, 144:162-171.
-
(2003)
J. Struct. Biol.
, vol.144
, pp. 162-171
-
-
Yang, S.1
Yu, X.2
Galkin, V.E.3
Egelman, E.H.4
-
78
-
-
84863276609
-
UCSF Chimera, MODELLER, and IMP: an integrated modeling system
-
Yang Z., Lasker K., Schneidman-Duhovny D., Webb B., Huang C.C., et al. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J. Struct. Biol. 2012, 179:269-278.
-
(2012)
J. Struct. Biol.
, vol.179
, pp. 269-278
-
-
Yang, Z.1
Lasker, K.2
Schneidman-Duhovny, D.3
Webb, B.4
Huang, C.C.5
-
79
-
-
75149145980
-
Mechanism of folding chamber closure in a group II chaperonin
-
Zhang J., Baker M.L., Schroder G.F., Douglas N.R., Reissmann S., et al. Mechanism of folding chamber closure in a group II chaperonin. Nature 2010, 463:379-383.
-
(2010)
Nature
, vol.463
, pp. 379-383
-
-
Zhang, J.1
Baker, M.L.2
Schroder, G.F.3
Douglas, N.R.4
Reissmann, S.5
-
80
-
-
41949099222
-
Towards atomic resolution structural determination by single-particle cryo-electron microscopy
-
Zhou Z.H. Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Curr. Opin. Struct. Biol. 2008, 18:218-228.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 218-228
-
-
Zhou, Z.H.1
-
81
-
-
0031345518
-
L-BFGS- B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale bound constrained optimization
-
Zhu C., Byrd R.H., Nocedal J. L-BFGS- B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale bound constrained optimization. ACM Trans. Math. Software 1997, 23:550-560.
-
(1997)
ACM Trans. Math. Software
, vol.23
, pp. 550-560
-
-
Zhu, C.1
Byrd, R.H.2
Nocedal, J.3
-
82
-
-
77649336168
-
Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement
-
Zhu J., Cheng L., Fang Q., Zhou Z.H., Honig B. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J. Mol. Biol. 2010, 397:835-851.
-
(2010)
J. Mol. Biol.
, vol.397
, pp. 835-851
-
-
Zhu, J.1
Cheng, L.2
Fang, Q.3
Zhou, Z.H.4
Honig, B.5
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