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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: More and better reference data for improved all-atom structure validation.
Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. Williams CJ, et al. Among authors: headd jj. Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27. Protein Sci. 2018. PMID: 29067766 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.
Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS. Headd JJ, et al. J Struct Funct Genomics. 2009 Mar;10(1):83-93. doi: 10.1007/s10969-008-9045-8. Epub 2008 Nov 11. J Struct Funct Genomics. 2009. PMID: 19002604 Free PMC article.
Protein-protein interfaces: properties, preferences, and projections.
Headd JJ, Ban YE, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Headd JJ, et al. J Proteome Res. 2007 Jul;6(7):2576-86. doi: 10.1021/pr070018+. Epub 2007 Jun 2. J Proteome Res. 2007. PMID: 17542628
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: headd jj. 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.
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.
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.
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. Afonine PV, et al. Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16. Acta Crystallogr D Biol Crystallogr. 2012. PMID: 22505256 Free PMC article.
Improved low-resolution crystallographic refinement with Phenix and Rosetta.
DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. DiMaio F, et al. Among authors: headd jj. Nat Methods. 2013 Nov;10(11):1102-4. doi: 10.1038/nmeth.2648. Epub 2013 Sep 29. Nat Methods. 2013. PMID: 24076763 Free PMC article.
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