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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: richardson js, richardson dc. 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.
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.
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: richardson js, richardson dc. 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. Among authors: richardson js, richardson dc. 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: richardson js, richardson dc. 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.
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. Liebschner D, et al. Among authors: richardson js, richardson dc. Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877. doi: 10.1107/S2059798319011471. Epub 2019 Oct 2. Acta Crystallogr D Struct Biol. 2019. PMID: 31588918 Free PMC article.
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.
Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. Afonine PV, et al. Among authors: richardson js, richardson dc. J Appl Crystallogr. 2010 Aug 1;43(Pt 4):669-676. doi: 10.1107/S0021889810015608. Epub 2010 May 22. J Appl Crystallogr. 2010. PMID: 20648263 Free PMC article.
Global data set of long-term summertime vertical temperature profiles in 153 lakes.
Pilla RM, Mette EM, Williamson CE, Adamovich BV, Adrian R, Anneville O, Balseiro E, Ban S, Chandra S, Colom-Montero W, Devlin SP, Dix MA, Dokulil MT, Feldsine NA, Feuchtmayr H, Fogarty NK, Gaiser EE, Girdner SF, González MJ, Hambright KD, Hamilton DP, Havens K, Hessen DO, Hetzenauer H, Higgins SN, Huttula TH, Huuskonen H, Isles PDF, Joehnk KD, Keller WB, Klug J, Knoll LB, Korhonen J, Korovchinsky NM, Köster O, Kraemer BM, Leavitt PR, Leoni B, Lepori F, Lepskaya EV, Lottig NR, Luger MS, Maberly SC, MacIntyre S, McBride C, McIntyre P, Melles SJ, Modenutti B, Müller-Navarra DC, Pacholski L, Paterson AM, Pierson DC, Pislegina HV, Plisnier PD, Richardson DC, Rimmer A, Rogora M, Rogozin DY, Rusak JA, Rusanovskaya OO, Sadro S, Salmaso N, Saros JE, Sarvala J, Saulnier-Talbot É, Schindler DE, Shimaraeva SV, Silow EA, Sitoki LM, Sommaruga R, Straile D, Strock KE, Swain H, Tallant JM, Thiery W, Timofeyev MA, Tolomeev AP, Tominaga K, Vanni MJ, Verburg P, Vinebrooke RD, Wanzenböck J, Weathers K, Weyhenmeyer GA, Zadereev ES, Zhukova TV. Pilla RM, et al. Among authors: richardson dc. Sci Data. 2021 Aug 4;8(1):200. doi: 10.1038/s41597-021-00983-y. Sci Data. 2021. PMID: 34349102 Free PMC article.
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