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Scientific benchmarks for guiding macromolecular energy function improvement.
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B. Leaver-Fay A, et al. Among authors: richardson js. Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0. Methods Enzymol. 2013. PMID: 23422428 Free PMC article.
Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Lovell SC, et al. Among authors: richardson js, richardson dc. Proteins. 2003 Feb 15;50(3):437-50. doi: 10.1002/prot.10286. Proteins. 2003. PMID: 12557186
A test of enhancing model accuracy in high-throughput crystallography.
Arendall WB 3rd, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, Liu ZJ, Rose JP, Carson WM, Luo M, Richardson DC, Wang BC. Arendall WB 3rd, et al. Among authors: richardson js, richardson dc. J Struct Funct Genomics. 2005;6(1):1-11. doi: 10.1007/s10969-005-3138-4. J Struct Funct Genomics. 2005. PMID: 15965733
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: richardson js, richardson dc. 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. Among authors: richardson js, richardson dc. 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.
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: richardson js, richardson dc. 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.
337 results