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For: Chen YW, Dodson EJ, Kleywegt GJ. Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures. Structure 2000;8:R213-20. [PMID: 11080645 DOI: 10.1016/s0969-2126(00)00524-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Caldararu O, Blundell TL, Kepp KP. A base measure of precision for protein stability predictors: structural sensitivity. BMC Bioinformatics 2021;22:88. [PMID: 33632133 PMCID: PMC7908712 DOI: 10.1186/s12859-021-04030-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/15/2021] [Indexed: 01/17/2023]  Open
2
Sánchez Rodríguez F, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ. Helical ensembles outperform ideal helices in molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020;76:962-970. [PMID: 33021498 PMCID: PMC7543657 DOI: 10.1107/s205979832001133x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/18/2020] [Indexed: 03/21/2023]
3
Hatti KS, McCoy AJ, Oeffner RD, Sammito MD, Read RJ. Factors influencing estimates of coordinate error for molecular replacement. Acta Crystallogr D Struct Biol 2020;76:19-27. [PMID: 31909740 PMCID: PMC6939440 DOI: 10.1107/s2059798319015730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/21/2019] [Indexed: 11/24/2022]  Open
4
Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard CC, Wojdyr M, Shepard W, Rigden DJ, Keegan RM. Using Phaser and ensembles to improve the performance of SIMBAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020;76:1-8. [PMID: 31909738 PMCID: PMC6939438 DOI: 10.1107/s2059798319015031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/06/2019] [Indexed: 01/07/2023]
5
Keegan RM, McNicholas SJ, Thomas JMH, Simpkin AJ, Simkovic F, Uski V, Ballard CC, Winn MD, Wilson KS, Rigden DJ. Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. Acta Crystallogr D Struct Biol 2018;74:167-182. [PMID: 29533225 PMCID: PMC5947758 DOI: 10.1107/s2059798318003455] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/27/2018] [Indexed: 01/21/2023]  Open
6
Calderone V, Fragai M, Luchinat C. When molecular replacement has no trivial solution: The importance of model editing in human S100Z X-ray structure solution. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.06.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
7
Shrestha R, Zhang KYJ. A fragmentation and reassembly method for ab initio phasing. ACTA ACUST UNITED AC 2015;71:304-12. [PMID: 25664740 DOI: 10.1107/s1399004714025449] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022]
8
Zhang W, Zhang T, Zhang H, Hao Q. Crystallographic phasing with NMR models: an envelope approach. ACTA ACUST UNITED AC 2014;70:1977-82. [DOI: 10.1107/s1399004714009754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/30/2014] [Indexed: 11/10/2022]
9
Scapin G. Molecular replacement then and now. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013;69:2266-75. [PMID: 24189239 PMCID: PMC3817701 DOI: 10.1107/s0907444913011426] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/26/2013] [Indexed: 01/22/2023]
10
Bibby J, Keegan RM, Mayans O, Winn MD, Rigden DJ. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013;69:2194-201. [PMID: 24189230 PMCID: PMC3817692 DOI: 10.1107/s0907444913018453] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/03/2013] [Indexed: 12/27/2022]
11
Anderson JS, Hernández G, LeMaster DM. Assessing the chemical accuracy of protein structures via peptide acidity. Biophys Chem 2012. [PMID: 23182463 DOI: 10.1016/j.bpc.2012.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung LW. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012;68:861-70. [PMID: 22751672 PMCID: PMC3388814 DOI: 10.1107/s0907444912015636] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 04/10/2012] [Indexed: 11/14/2022]
13
Scott WG. Challenges and surprises that arise with nucleic acids during model building and refinement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012;68:441-5. [PMID: 22505264 PMCID: PMC3322603 DOI: 10.1107/s0907444912001084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 01/10/2012] [Indexed: 11/11/2022]
14
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. ACTA ACUST UNITED AC 2012;13:81-90. [PMID: 22418934 PMCID: PMC3375004 DOI: 10.1007/s10969-012-9129-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 02/07/2012] [Indexed: 11/03/2022]
15
Mao B, Guan R, Montelione GT. Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure 2011;19:757-66. [PMID: 21645849 PMCID: PMC3612016 DOI: 10.1016/j.str.2011.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/07/2011] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
16
Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE. SAD phasing using iodide ions in a high-throughput structural genomics environment. ACTA ACUST UNITED AC 2011;12:83-95. [PMID: 21359836 PMCID: PMC3123459 DOI: 10.1007/s10969-011-9101-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 02/14/2011] [Indexed: 03/16/2023]
17
Robertson MP, Chi YI, Scott WG. Solving novel RNA structures using only secondary structural fragments. Methods 2010;52:168-72. [PMID: 20541014 PMCID: PMC2948636 DOI: 10.1016/j.ymeth.2010.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Indexed: 10/19/2022]  Open
18
Haikarainen T, Tsou CC, Wu JJ, Papageorgiou AC. Crystal structures of Streptococcus pyogenes Dpr reveal a dodecameric iron-binding protein with a ferroxidase site. J Biol Inorg Chem 2009;15:183-94. [PMID: 19727858 DOI: 10.1007/s00775-009-0582-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 08/14/2009] [Indexed: 11/28/2022]
19
Buehler A, Urzhumtseva L, Lunin VY, Urzhumtsev A. Cluster analysis for phasing with molecular replacement: a feasibility study. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009;65:644-50. [PMID: 19564684 PMCID: PMC2703570 DOI: 10.1107/s090744490900969x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 03/16/2009] [Indexed: 11/24/2022]
20
Szymczyna BR, Taurog RE, Young MJ, Snyder JC, Johnson JE, Williamson JR. Synergy of NMR, computation, and X-ray crystallography for structural biology. Structure 2009;17:499-507. [PMID: 19368883 PMCID: PMC2705668 DOI: 10.1016/j.str.2009.03.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2009] [Revised: 02/22/2009] [Accepted: 03/03/2009] [Indexed: 11/26/2022]
21
Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins 2009;75:147-67. [PMID: 18816799 PMCID: PMC2878636 DOI: 10.1002/prot.22229] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
22
Das R, Baker D. Prospects for de novo phasing with de novo protein models. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009;65:169-75. [PMID: 19171972 PMCID: PMC2631639 DOI: 10.1107/s0907444908020039] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 07/01/2008] [Indexed: 11/10/2022]
23
Robertson MP, Scott WG. A general method for phasing novel complex RNA crystal structures without heavy-atom derivatives. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2008;D64:738-44. [PMID: 18566509 PMCID: PMC2507861 DOI: 10.1107/s0907444908011578] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 04/22/2008] [Indexed: 11/12/2022]
24
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature 2007;450:259-64. [PMID: 17934447 PMCID: PMC2504711 DOI: 10.1038/nature06249] [Citation(s) in RCA: 235] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 09/13/2007] [Indexed: 11/09/2022]
25
Kaneko T, Tanaka N, Kumasaka T. Crystal structures of RsbQ, a stress-response regulator in Bacillus subtilis. Protein Sci 2005;14:558-65. [PMID: 15632289 PMCID: PMC2253412 DOI: 10.1110/ps.041170005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
26
Kaneko T, Kumasaka T, Ganbe T, Sato T, Miyazawa K, Kitamura N, Tanaka N. Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain. J Biol Chem 2003;278:48162-8. [PMID: 13129930 DOI: 10.1074/jbc.m306677200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
27
Fujii Y, Okuda D, Fujimoto Z, Horii K, Morita T, Mizuno H. Crystal Structure of Trimestatin, a Disintegrin Containing a Cell Adhesion Recognition Motif RGD. J Mol Biol 2003;332:1115-22. [PMID: 14499613 DOI: 10.1016/s0022-2836(03)00991-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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