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Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):391-403. doi: 10.1107/S090744491104978X. Epub 2012 Mar 16.


Automated structure solution with the PHENIX suite.

Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.

Methods Mol Biol. 2008;426:419-35. doi: 10.1007/978-1-60327-058-8_28.


Model morphing and sequence assignment after molecular replacement.

Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung LW.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2244-50. doi: 10.1107/S0907444913017770. Epub 2013 Oct 18.


The Phenix software for automated determination of macromolecular structures.

Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.

Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.


Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):61-9. Epub 2007 Dec 5.


On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination.

Panjikar S, Parthasarathy V, Lamzin VS, Weiss MS, Tucker PA.

Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1089-97. doi: 10.1107/S0907444909029643. Epub 2009 Sep 16.


Towards automated crystallographic structure refinement with phenix.refine.

Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16.


Deformable complex network for refining low-resolution X-ray structures.

Zhang C, Wang Q, Ma J.

Acta Crystallogr D Biol Crystallogr. 2015 Nov;71(Pt 11):2150-7. doi: 10.1107/S139900471501528X. Epub 2015 Oct 27.


Automated identification of elemental ions in macromolecular crystal structures.

Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1104-14. doi: 10.1107/S1399004714001308. Epub 2014 Mar 20.


Crystallization and preliminary X-ray crystallographic analysis of the amylomaltase from Corynebacterium glutamicum.

Srisimarat W, Murakami S, Pongsawasdi P, Krusong K.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Sep;69(Pt 9):1004-6. doi: 10.1107/S1744309113020319. Epub 2013 Aug 19.


CaspR: a web server for automated molecular replacement using homology modelling.

Claude JB, Suhre K, Notredame C, Claverie JM, Abergel C.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9.


The JCSG MR pipeline: optimized alignments, multiple models and parallel searches.

Schwarzenbacher R, Godzik A, Jaroszewski L.

Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):133-40. Epub 2007 Dec 5.


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 ZH, Honig B.

J Mol Biol. 2010 Apr 2;397(3):835-51. doi: 10.1016/j.jmb.2010.01.041. Epub 2010 Jan 28.


Using SAD data in Phaser.

Read RJ, McCoy AJ.

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-44. doi: 10.1107/S0907444910051371. Epub 2011 Mar 5.


Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus.

Fadouloglou VE, Kapanidou M, Agiomirgianaki A, Arnaouteli S, Bouriotis V, Glykos NM, Kokkinidis M.

Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):276-83. doi: 10.1107/S0907444912045829. Epub 2013 Jan 19.


Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.

Smart OS, Womack TO, Flensburg C, Keller P, Paciorek W, Sharff A, Vonrhein C, Bricogne G.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):368-80. doi: 10.1107/S0907444911056058. Epub 2012 Mar 16.


Crystal Structure of Amylomaltase from Corynebacterium glutamicum.

Joo S, Kim S, Seo H, Kim KJ.

J Agric Food Chem. 2016 Jul 20;64(28):5662-70. doi: 10.1021/acs.jafc.6b02296. Epub 2016 Jul 8.


EDM-DEDM and protein crystal structure solution.

Caliandro R, Carrozzini B, Cascarano GL, Giacovazzo C, Mazzone AM, Siliqi D.

Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):477-84. doi: 10.1107/S0907444909008609. Epub 2009 Apr 18. Review.


Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1.

Akey DL, Brown WC, Konwerski JR, Ogata CM, Smith JL.

Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2719-29. doi: 10.1107/S1399004714017556. Epub 2014 Sep 27.


REdiii: a pipeline for automated structure solution.

Bohn MF, Schiffer CA.

Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1059-67. doi: 10.1107/S139900471500303X. Epub 2015 Apr 24.

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