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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. Among authors: kapral gj. 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.
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. Kapral GJ, et al. Nucleic Acids Res. 2014 Nov 10;42(20):12833-46. doi: 10.1093/nar/gku992. Epub 2014 Oct 17. Nucleic Acids Res. 2014. PMID: 25326328 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. Among authors: kapral gj. Proteins. 2009;77 Suppl 9(Suppl 9):29-49. doi: 10.1002/prot.22551. Proteins. 2009. PMID: 19731372 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. Among authors: kapral gj. 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.
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. Among authors: kapral gj. 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.
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. Among authors: kapral gj. 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.
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J. Wang X, et al. J Math Biol. 2008 Jan;56(1-2):253-78. doi: 10.1007/s00285-007-0082-x. Epub 2007 Mar 31. J Math Biol. 2008. PMID: 17401565 Free PMC article.
Small Molecule-Based Pattern Recognition To Classify RNA Structure.
Eubanks CS, Forte JE, Kapral GJ, Hargrove AE. Eubanks CS, et al. Among authors: kapral gj. J Am Chem Soc. 2017 Jan 11;139(1):409-416. doi: 10.1021/jacs.6b11087. Epub 2016 Dec 22. J Am Chem Soc. 2017. PMID: 28004925 Free PMC article.
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM; RNA Ontology Consortium. Richardson JS, et al. Among authors: kapral gj. RNA. 2008 Mar;14(3):465-81. doi: 10.1261/rna.657708. Epub 2008 Jan 11. RNA. 2008. PMID: 18192612 Free PMC article.
Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.
Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH. Dunkle JA, et al. Among authors: kapral gj. Science. 2011 May 20;332(6032):981-4. doi: 10.1126/science.1202692. Science. 2011. PMID: 21596992 Free PMC article.
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