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MolProbity: all-atom structure validation for macromolecular crystallography.
Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. Chen VB, et al. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21. doi: 10.1107/S0907444909042073. Epub 2009 Dec 21. Acta Crystallogr D Biol Crystallogr. 2010. PMID: 20057044 Free PMC article.
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, Richardson DC. Davis IW, et al. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83. doi: 10.1093/nar/gkm216. Epub 2007 Apr 22. Nucleic Acids Res. 2007. PMID: 17452350 Free PMC article.
KinImmerse: Macromolecular VR for NMR ensembles.
Block JN, Zielinski DJ, Chen VB, Davis IW, Vinson EC, Brady R, Richardson JS, Richardson DC. Block JN, et al. Source Code Biol Med. 2009 Feb 17;4:3. doi: 10.1186/1751-0473-4-3. Source Code Biol Med. 2009. PMID: 19222844 Free PMC article.
The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.
Keedy DA, Williams CJ, Headd JJ, Arendall WB 3rd, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. Keedy DA, et al. Proteins. 2009;77 Suppl 9(Suppl 9):29-49. doi: 10.1002/prot.22551. Proteins. 2009. PMID: 19731372 Free PMC article.
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. Adams PD, et al. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. doi: 10.1107/S0907444909052925. Epub 2010 Jan 22. Acta Crystallogr D Biol Crystallogr. 2010. PMID: 20124702 Free PMC article.
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. Adams PD, et al. Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29. Methods. 2011. PMID: 21821126 Free PMC article.
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.
Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Headd JJ, et al. Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):381-90. doi: 10.1107/S0907444911047834. Epub 2012 Mar 16. Acta Crystallogr D Biol Crystallogr. 2012. PMID: 22505258 Free PMC article.
Graphical tools for macromolecular crystallography in PHENIX.
Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD. Echols N, et al. Among authors: chen vb. J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. doi: 10.1107/S0021889812017293. Epub 2012 May 16. J Appl Crystallogr. 2012. PMID: 22675231 Free PMC article.
Probing conformational changes in human DNA topoisomerase IIα by pulsed alkylation mass spectrometry.
Chen YT, Collins TR, Guan Z, Chen VB, Hsieh TS. Chen YT, et al. Among authors: chen vb. J Biol Chem. 2012 Jul 20;287(30):25660-8. doi: 10.1074/jbc.M112.377606. Epub 2012 Jun 7. J Biol Chem. 2012. PMID: 22679013 Free PMC article.
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