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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.
Alternate states of proteins revealed by detailed energy landscape mapping.
Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Tyka MD, et al. J Mol Biol. 2011 Jan 14;405(2):607-18. doi: 10.1016/j.jmb.2010.11.008. Epub 2010 Nov 10. J Mol Biol. 2011. PMID: 21073878 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.
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.
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: keedy da. 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 role of local backrub motions in evolved and designed mutations.
Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. Keedy DA, et al. PLoS Comput Biol. 2012;8(8):e1002629. doi: 10.1371/journal.pcbi.1002629. Epub 2012 Aug 2. PLoS Comput Biol. 2012. PMID: 22876172 Free PMC article.
OSPREY: protein design with ensembles, flexibility, and provable algorithms.
Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. Gainza P, et al. Methods Enzymol. 2013;523:87-107. doi: 10.1016/B978-0-12-394292-0.00005-9. Methods Enzymol. 2013. PMID: 23422427 Free PMC article.
Algorithm for backrub motions in protein design.
Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Georgiev I, et al. Bioinformatics. 2008 Jul 1;24(13):i196-204. doi: 10.1093/bioinformatics/btn169. Bioinformatics. 2008. PMID: 18586714 Free PMC article.
Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.
Keedy DA, Fraser JS, van den Bedem H. Keedy DA, et al. PLoS Comput Biol. 2015 Oct 27;11(10):e1004507. doi: 10.1371/journal.pcbi.1004507. eCollection 2015 Oct. PLoS Comput Biol. 2015. PMID: 26506617 Free PMC article.
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