-
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., Echols N., Headd J.J., Hung L.W., Kapral G.J., Grosse-Kunstleve R.W., McCoy A.J., Moriarty N.W., Oeffner R., Read R.J., Richardson D.C., Richardson J.S., Terwillinger T.C., Zwart P.H. 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
Echols, N.6
Headd, J.J.7
Hung, L.W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
McCoy, A.J.11
Moriarty, N.W.12
Oeffner, R.13
Read, R.J.14
Richardson, D.C.15
Richardson, J.S.16
Terwillinger, T.C.17
Zwart, P.H.18
-
2
-
-
35548993306
-
The Phenix refinement framework
-
contibution 8.
-
Afonine, P.V., Grosse-Kunstleve, R.E., Adams, P.D., 2005. The Phenix refinement framework. CCP4 Newsl. 42, contibution 8.
-
(2005)
CCP4 Newsl.
, vol.42
-
-
Afonine, P.V.1
Grosse-Kunstleve, R.E.2
Adams, P.D.3
-
3
-
-
34948885722
-
Crystal structure of T4 endonuclease VII resolving a Holliday junction
-
Biertumpfel C., Yang W., Suck D. Crystal structure of T4 endonuclease VII resolving a Holliday junction. Nature 2007, 449:616-620.
-
(2007)
Nature
, vol.449
, pp. 616-620
-
-
Biertumpfel, C.1
Yang, W.2
Suck, D.3
-
4
-
-
9944227232
-
Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1
-
Bruning J., Shamoo Y. Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1. Structure 2004, 12:2209-2219.
-
(2004)
Structure
, vol.12
, pp. 2209-2219
-
-
Bruning, J.1
Shamoo, Y.2
-
5
-
-
0028103275
-
The CCP4 suite: programs for protein crystallography
-
Collaborative Computational Project, Number 4.
-
Collaborative Computational Project, Number 4, 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763.
-
(1994)
Acta Crystallogr. D Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
6
-
-
0035949599
-
A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems
-
Dalrymple B., Kongsuwan K., Wijffels G., Dixon N., Jennings P. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc. Natl. Acad. Sci. USA 2001, 98:11627-11632.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 11627-11632
-
-
Dalrymple, B.1
Kongsuwan, K.2
Wijffels, G.3
Dixon, N.4
Jennings, P.5
-
7
-
-
34547592557
-
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
-
Davis I., Leaver-Fay A., Chen V., Block J., Kapral G., Wang X., Murray L., Arendall W.r., Snoeyink J., Richardson J., Richardson D. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007, 35:W375-W383.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Davis, I.1
Leaver-Fay, A.2
Chen, V.3
Block, J.4
Kapral, G.5
Wang, X.6
Murray, L.7
Arendall, W.8
Snoeyink, J.9
Richardson, J.10
Richardson, D.11
-
9
-
-
40549087271
-
On the mechanism of loading the PCNA sliding clamp by RFC
-
Dionne I., Brown N.J., Woodgate R., Bell S.D. On the mechanism of loading the PCNA sliding clamp by RFC. Mol. Microbiol. 2008, 68:216-222.
-
(2008)
Mol. Microbiol.
, vol.68
, pp. 216-222
-
-
Dionne, I.1
Brown, N.J.2
Woodgate, R.3
Bell, S.D.4
-
10
-
-
0037251411
-
A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus
-
Dionne I., Nookala R.K., Jackson S.P., Doherty A.J., Bell S.D. A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Cell 2003, 11:275-282.
-
(2003)
Mol. Cell
, vol.11
, pp. 275-282
-
-
Dionne, I.1
Nookala, R.K.2
Jackson, S.P.3
Doherty, A.J.4
Bell, S.D.5
-
11
-
-
33750008990
-
Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity
-
Doré A., Kilkenny M., Jones S., Oliver A., Roe S., Bell S., Pearl L. Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity. Nucleic Acids Res. 2006, 34:4515-4526.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 4515-4526
-
-
Doré, A.1
Kilkenny, M.2
Jones, S.3
Oliver, A.4
Roe, S.5
Bell, S.6
Pearl, L.7
-
12
-
-
67649111979
-
Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex-implications for clamp loading and regulation
-
Doré A., Kilkenny M., Rzechorzek N., Pearl L. Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex-implications for clamp loading and regulation. Mol. Cell 2009, 34:735-745.
-
(2009)
Mol. Cell
, vol.34
, pp. 735-745
-
-
Doré, A.1
Kilkenny, M.2
Rzechorzek, N.3
Pearl, L.4
-
13
-
-
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
-
16
-
-
0030592544
-
Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA
-
Gulbis J.M., Kelman Z., Hurwitz J., O'Donnell M., Kuriyan J. Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 1996, 87:297-306.
-
(1996)
Cell
, vol.87
, pp. 297-306
-
-
Gulbis, J.M.1
Kelman, Z.2
Hurwitz, J.3
O'Donnell, M.4
Kuriyan, J.5
-
17
-
-
33751419716
-
Surviving the breakup: the DNA damage checkpoint
-
Harrison J.C., Haber J.E. Surviving the breakup: the DNA damage checkpoint. Annu. Rev. Genet. 2006, 40:209-235.
-
(2006)
Annu. Rev. Genet.
, vol.40
, pp. 209-235
-
-
Harrison, J.C.1
Haber, J.E.2
-
18
-
-
67449103688
-
Structural basis for novel interactions between human translesion synthesis polymerases and proliferating cell nuclear antigen
-
Hishiki A., Hashimoto H., Hanafusa T., Kamei K., Ohashi E., Shimizu T., Ohmori H., Sato M. Structural basis for novel interactions between human translesion synthesis polymerases and proliferating cell nuclear antigen. J. Biol. Chem. 2009, 284:10552-10560.
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 10552-10560
-
-
Hishiki, A.1
Hashimoto, H.2
Hanafusa, T.3
Kamei, K.4
Ohashi, E.5
Shimizu, T.6
Ohmori, H.7
Sato, M.8
-
19
-
-
49749129283
-
Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening
-
Hlinkova V., Xing G., Bauer J., Shin Y.J., Dionne I., Rajashankar K.R., Bell S.D., Ling H. Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening. Acta. Crystallogr. D Biol. Crystallogr. 2008, 64:941-949.
-
(2008)
Acta. Crystallogr. D Biol. Crystallogr.
, vol.64
, pp. 941-949
-
-
Hlinkova, V.1
Xing, G.2
Bauer, J.3
Shin, Y.J.4
Dionne, I.5
Rajashankar, K.R.6
Bell, S.D.7
Ling, H.8
-
20
-
-
0037068455
-
RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO
-
Hoege C., Pfander B., Moldovan G., Pyrowolakis G., Jentsch S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 2002, 419:135-141.
-
(2002)
Nature
, vol.419
, pp. 135-141
-
-
Hoege, C.1
Pfander, B.2
Moldovan, G.3
Pyrowolakis, G.4
Jentsch, S.5
-
21
-
-
34247346621
-
Specific interactions of three proliferating cell nuclear antigens with replication-related proteins in Aeropyrum pernix
-
Imamura K., Fukunaga K., Kawarabayasi Y., Ishino Y. Specific interactions of three proliferating cell nuclear antigens with replication-related proteins in Aeropyrum pernix. Mol. Microbiol. 2007, 64:308-318.
-
(2007)
Mol. Microbiol.
, vol.64
, pp. 308-318
-
-
Imamura, K.1
Fukunaga, K.2
Kawarabayasi, Y.3
Ishino, Y.4
-
22
-
-
33749033347
-
The replication clamp-loading machine at work in the three domains of life
-
Indiani C., O'Donnell M. The replication clamp-loading machine at work in the three domains of life. Nat. Rev. Mol. Cell Biol. 2006, 7:751-761.
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 751-761
-
-
Indiani, C.1
O'Donnell, M.2
-
23
-
-
74549201624
-
Purification, crystallization and preliminary X-ray analysis of the PCNA2-PCNA3 complex from Sulfolobus tokodaii strain 7
-
Kawai A., Higuchi S., Tsunoda M., Nakamura K., Miyamoto S. Purification, crystallization and preliminary X-ray analysis of the PCNA2-PCNA3 complex from Sulfolobus tokodaii strain 7. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2009, 65:1282-1284.
-
(2009)
Acta Crystallogr. F Struct. Biol. Cryst. Commun.
, vol.65
, pp. 1282-1284
-
-
Kawai, A.1
Higuchi, S.2
Tsunoda, M.3
Nakamura, K.4
Miyamoto, S.5
-
24
-
-
13844316580
-
Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design
-
Kontopidis G., Wu S., Zheleva D., Taylor P., McInnes C., Lane D., Fischer P., Walkinshaw M. Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design. Proc. Natl. Acad. Sci. USA 2005, 102:1871-1876.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 1871-1876
-
-
Kontopidis, G.1
Wu, S.2
Zheleva, D.3
Taylor, P.4
McInnes, C.5
Lane, D.6
Fischer, P.7
Walkinshaw, M.8
-
25
-
-
0035124442
-
Automated matching of high- and low-resolution structural models
-
Kozin M.B., Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Cryst. 2001, 34:33-41.
-
(2001)
J. Appl. Cryst.
, vol.34
, pp. 33-41
-
-
Kozin, M.B.1
Svergun, D.I.2
-
26
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel E., Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2256-2268.
-
(2004)
Acta Crystallogr. D Biol. Crystallogr.
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
27
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E., Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007, 372:774-797.
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
28
-
-
0027772959
-
Shape complementarity at protein/protein interfaces
-
Lawrence M., Colman P. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 1993, 234:946-950.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 946-950
-
-
Lawrence, M.1
Colman, P.2
-
29
-
-
0003076963
-
Recent changes to the MOSFLM package for processing film and image plate data. Jnt. CCP4/ESF-EACBM Newsl
-
Leslie A.G.W. Recent changes to the MOSFLM package for processing film and image plate data. Jnt. CCP4/ESF-EACBM Newsl. Protein Crystallogr 1992, 23:27-33.
-
(1992)
Protein Crystallogr
, vol.23
, pp. 27-33
-
-
Leslie, A.G.W.1
-
30
-
-
52949091518
-
Spatial subunit distribution and in vitro functions of the novel trimeric PCNA complex from Sulfolobus tokodaii
-
Lu S., Li Z., Wang Z., Ma X., Sheng D., Ni J., Shen Y. Spatial subunit distribution and in vitro functions of the novel trimeric PCNA complex from Sulfolobus tokodaii. Biochem. Biophys. Res. Commun. 2008, 376:369-374.
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.376
, pp. 369-374
-
-
Lu, S.1
Li, Z.2
Wang, Z.3
Ma, X.4
Sheng, D.5
Ni, J.6
Shen, Y.7
-
31
-
-
0035107856
-
Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus
-
Matsumiya S., Ishino Y., Morikawa K. Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus. Protein Sci. 2001, 10:17-23.
-
(2001)
Protein Sci.
, vol.10
, pp. 17-23
-
-
Matsumiya, S.1
Ishino, Y.2
Morikawa, K.3
-
32
-
-
34447508216
-
Phaser crystallographic software
-
McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 2007, 40:658-674.
-
(2007)
J. Appl. Crystallogr.
, 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
-
33
-
-
33747882922
-
PCNA controls establishment of sister chromatid cohesion during S phase
-
Moldovan G.L., Pfander B., Jentsch S. PCNA controls establishment of sister chromatid cohesion during S phase. Mol. Cell 2006, 23:723-732.
-
(2006)
Mol. Cell
, vol.23
, pp. 723-732
-
-
Moldovan, G.L.1
Pfander, B.2
Jentsch, S.3
-
34
-
-
34249066085
-
PCNA, the maestro of the replication fork
-
Moldovan G.L., Pfander B., Jentsch S. PCNA, the maestro of the replication fork. Cell 2007, 129:665-679.
-
(2007)
Cell
, vol.129
, pp. 665-679
-
-
Moldovan, G.L.1
Pfander, B.2
Jentsch, S.3
-
35
-
-
22944474665
-
SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase
-
Pfander B., Moldovan G., Sacher M., Hoege C., Jentsch S. SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature 2005, 436:428-433.
-
(2005)
Nature
, vol.436
, pp. 428-433
-
-
Pfander, B.1
Moldovan, G.2
Sacher, M.3
Hoege, C.4
Jentsch, S.5
-
36
-
-
20144367589
-
Structural basis for recruitment of human flap endonuclease 1 to PCNA
-
Sakurai S., Kitano K., Yamaguchi H., Hamada K., Okada K., Fukuda K., Uchida M., Ohtsuka E., Morioka H., Hakoshima T. Structural basis for recruitment of human flap endonuclease 1 to PCNA. EMBO J. 2005, 24:683-693.
-
(2005)
EMBO J.
, vol.24
, pp. 683-693
-
-
Sakurai, S.1
Kitano, K.2
Yamaguchi, H.3
Hamada, K.4
Okada, K.5
Fukuda, K.6
Uchida, M.7
Ohtsuka, E.8
Morioka, H.9
Hakoshima, T.10
-
37
-
-
3943107573
-
Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints
-
Sancar A., Lindsey-Boltz L., Unsal-Kaçmaz K., Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 2004, 73:39-85.
-
(2004)
Annu. Rev. Biochem.
, vol.73
, pp. 39-85
-
-
Sancar, A.1
Lindsey-Boltz, L.2
Unsal-Kaçmaz, K.3
Linn, S.4
-
38
-
-
67449103064
-
Crystal structure of the human rad9-hus1-rad1 clamp
-
Sohn S., Cho Y. Crystal structure of the human rad9-hus1-rad1 clamp. J Mol Biol 2009, 390:490-502.
-
(2009)
J Mol Biol
, vol.390
, pp. 490-502
-
-
Sohn, S.1
Cho, Y.2
-
39
-
-
0141831006
-
Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation
-
Stelter P., Ulrich H. Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 2003, 425:188-191.
-
(2003)
Nature
, vol.425
, pp. 188-191
-
-
Stelter, P.1
Ulrich, H.2
-
40
-
-
33845627082
-
Cellular responses to DNA damage: one signal, multiple choices
-
Su T. Cellular responses to DNA damage: one signal, multiple choices. Annu. Rev. Genet. 2006, 40:187-208.
-
(2006)
Annu. Rev. Genet.
, vol.40
, pp. 187-208
-
-
Su, T.1
-
41
-
-
0026910457
-
Determination of the regularization parameter in indirect-transform methods using perceptual criteria
-
Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Cryst. 1992, 25:495-503.
-
(1992)
J. Appl. Cryst.
, vol.25
, pp. 495-503
-
-
Svergun, D.I.1
-
42
-
-
0033001996
-
Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
-
Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 1999, 76:2879-2886.
-
(1999)
Biophys. J.
, vol.76
, pp. 2879-2886
-
-
Svergun, D.I.1
-
43
-
-
0032569982
-
PCNA, a multifunctional ring on DNA
-
Tsurimoto T. PCNA, a multifunctional ring on DNA. Biochim. Biophys. Acta 1998, 1443:23-39.
-
(1998)
Biochim. Biophys. Acta
, vol.1443
, pp. 23-39
-
-
Tsurimoto, T.1
-
44
-
-
0037523309
-
The diverse spectrum of sliding clamp interacting proteins
-
Vivona J., Kelman Z. The diverse spectrum of sliding clamp interacting proteins. FEBS Lett. 2003, 546:167-172.
-
(2003)
FEBS Lett.
, vol.546
, pp. 167-172
-
-
Vivona, J.1
Kelman, Z.2
-
45
-
-
0037701585
-
Uniqueness of ab initio shape determination in small-angle scattering
-
Volkov V.V., Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crsyt. 2003, 36:860-864.
-
(2003)
J. Appl. Crsyt.
, vol.36
, pp. 860-864
-
-
Volkov, V.V.1
Svergun, D.I.2
-
46
-
-
0033777562
-
The puzzle of PCNA's many partners
-
Warbrick E. The puzzle of PCNA's many partners. Bioessays 2000, 22:997-1006.
-
(2000)
Bioessays
, vol.22
, pp. 997-1006
-
-
Warbrick, E.1
-
47
-
-
33749534839
-
Structure of the heterotrimeric PCNA from Sulfolobus solfataricus
-
Williams G.J., Johnson K., Rudolf J., McMahon S.A., Carter L., Oke M., Liu H., Taylor G.L., White M.F., Naismith J.H. Structure of the heterotrimeric PCNA from Sulfolobus solfataricus. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 2006, 62:944-948.
-
(2006)
Acta Crystallogr. F Struct. Biol. Cryst. Commun.
, vol.62
, pp. 944-948
-
-
Williams, G.J.1
Johnson, K.2
Rudolf, J.3
McMahon, S.A.4
Carter, L.5
Oke, M.6
Liu, H.7
Taylor, G.L.8
White, M.F.9
Naismith, J.H.10
-
48
-
-
58449104506
-
Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA
-
Xing G., Kirouac K., Shin Y.J., Bell S.D., Ling H. Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA. Mol. Microbiol. 2009, 71:678-691.
-
(2009)
Mol. Microbiol.
, vol.71
, pp. 678-691
-
-
Xing, G.1
Kirouac, K.2
Shin, Y.J.3
Bell, S.D.4
Ling, H.5
-
49
-
-
68949137117
-
Structure and functional implications of the human Rad9-Hus1-Rad1 cell cycle checkpoint complex
-
Xu M., Bai L., Gong Y., Xie W., Hang H.Y., Jiang T. Structure and functional implications of the human Rad9-Hus1-Rad1 cell cycle checkpoint complex. J. Biol. Chem. 2009, 284:20457-20461.
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 20457-20461
-
-
Xu, M.1
Bai, L.2
Gong, Y.3
Xie, W.4
Hang, H.Y.5
Jiang, T.6
|