Jane Shelby Richardson | Scholars@Duke

Jane Shelby Richardson
James B. Duke Professor of Medicine

3D structure of macromolecules; molecular graphics; protein folding and design; all-atom contacts; x-ray crystallography; structure validation.

Current Appointments & Affiliations

James B. Duke Professor of Medicine, Biochemistry, Basic Science Departments 1992
Professor of Biochemistry, Biochemistry, Basic Science Departments 1991

Contact Information

132 Nanaline H Duke, Durham, NC 27710
Duke Box 3711, Durham, NC 27710
jsr@kinemage.biochem.duke.edu (919) 684-6010
MolProbity validation
lab web site

Background
Education, Training, & Certifications
- M.A., Harvard University 1966
Recognition
In the News
- OCT 23, 2018
  
  Science's 'Master of Ribbon Diagrams' Celebrates 50 Years at Duke
- FEB 9, 2016 Scientific American
  
  Jane Richardson: Visualizing protein structures
- NOV 21, 2014 The Atlantic
  
  Jane Richardson: Driving force behind WikiProject Biophysics
Awards & Honors
Research
Selected Grants
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Occurrence and Functional Roles of High Energy Base Pairs in DNA awarded by National Institutes of Health 2015 - 2019
- PHENIX: New methods for automation in macromolecular crystallography awarded by Ernest Orlando Lawrence Berkeley National Laboratory 2006 - 2019
- Structural Biology and Biophysics Training Program awarded by National Institutes of Health 1994 - 2015
- New Kind of Quality Management for X-ray & NMR Models awarded by National Institutes of Health 2005 - 2015
- "Low-Resolution Interiors & Interfaces Can Achieve High-Resolution Accuracy" awarded by National Institutes of Health 2009 - 2014
- Automated NMR Assignment and Protein Structure Determination awarded by National Institutes of Health 2006 - 2012
- Inverse Kinematics, Sterics & Data - To Fit RNA Backbone awarded by National Institutes of Health 2005 - 2010
- Molecular mechanisms of nitrosative stress resistance awarded by National Institutes of Health 1999 - 2005
- Analysis and Design of Protein Structures awarded by National Institutes of Health 1984 - 2004
- All-Atom Contact Analysis in Improving Structure Quality awarded by National Institutes of Health 2001 - 2004
- Study Of Crystallization & Solution Properties Of Redesign awarded by National Aeronautics and Space Administration 1993 - 1998
- Analysis & Design Of Protein Structures awarded by National Institutes of Health 1984 - 1998
- Cancer Center Core Support Grant awarded by National Institutes of Health 1976 - 1998
- Comprehensive Cancer Center Core Support Grant awarded by National Institutes of Health 1976 - 1998
- Comprehensive Cancer Center Core Support Grant awarded by National Institutes of Health 1976 - 1998
- Study Of Crystallization And Solution Properties Of Redesi awarded by National Aeronautics and Space Administration 1993 - 1996
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Richardson JS, Williams CJ, Videau LL, Chen VB, Richardson DC. Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale. Journal of Structural Biology. 2018 Nov;204(2):301-312. PubMed Central PMCID: 30107233. Full Text
  - Wang Y, Shekhar M, Thifault D, Williams CJ, McGreevy R, Richardson J, Singharoy A, Tajkhorshid E. Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons. Journal of Structural Biology. 2018 Nov;204(2):319-328. PubMed Central PMCID: 30092279. Full Text
  - Richardson JS, Williams CJ, Hintze BJ, Chen VB, Prisant MG, Videau LL, Richardson DC. Model validation: local diagnosis, correction and when to quit. Acta Crystallographica. Section D, Structural Biology. 2018 Feb;74(Pt 2):132-142. PubMed Central PMCID: 29533239. Full Text
  - 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, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation. Protein Science : a Publication of the Protein Society. 2018 Jan;27(1):293-315. PubMed Central PMCID: 29067766. Full Text
  - Hintze BJ, Richardson JS, Richardson DC. Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallographica. Section D, Structural Biology. 2017 Oct 2;73(Pt 10):852-859. PubMed Central PMCID: 28994414. Full Text
  - Richardson JS, Videau LL, Williams CJ, Richardson DC. Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. Journal of molecular biology. 2017 May;429(9):1321-1335. PubMed PMID: 28336403. Full Text
  - Hintze BJ, Lewis SM, Richardson JS, Richardson DC. Molprobity's ultimate rotamer-library distributions for model validation. Proteins. 2016 Sep;84(9):1177-1189. PubMed Central PMCID: 27018641. Full Text
  - Hintze BJ, Lewis SM, Richardson JS, Richardson DC. Cover Image, Volume 84, Issue 9. Proteins: Structure, Function, and Bioinformatics. 2016 Sep;84(9):C1-C1. Full Text
  - Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Research. 2015 Apr;43(7):3420-3433. PubMed Central PMCID: 25813047. (Review) Full Text Open Access Copy
  - Jain S, Richardson DC, Richardson JS. Computational Methods for RNA Structure Validation and Improvement. Methods in Enzymology. 2015 Jan;558:181-212. PubMed Central PMCID: 26068742. Full Text Open Access Copy
  - Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic acids research. 2014 Nov;42(20):12833-12846. PubMed PMID: 25326328. Full Text Open Access Copy
  - Deis LN, Pemble CW, Qi Y, Hagarman A, Richardson DC, Richardson JS, Oas TG. Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Structure (London, England : 1993). 2014 Oct;22(10):1467-1477. PubMed Central PMCID: 25295398. Full Text Open Access Copy
  - Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 2014 Apr;70(Pt 4):1104-1114. PubMed Central PMCID: 24699654. Full Text
  - Richardson JS, Richardson DC. Biophysical highlights from 54 years of macromolecular crystallography. Biophysical journal. 2014 Feb;106(3):510-525. PubMed PMID: 24507592. (Review) Full Text
  - Richardson JS, Prisant MG, Richardson DC. Crystallographic model validation: from diagnosis to healing. Curr Opin Struct Biol. 2013 Oct;23(5):707-714. PubMed PMID: 24064406. (Review) Full Text Link to Item
  - Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Recommendations of the wwPDB NMR Validation Task Force. Structure (London, England : 1993). 2013 Sep;21(9):1563-1570. PubMed Central PMCID: 24010715. Full Text
  - Richardson J. An interview with Jane Richardson. Trends in biochemical sciences. 2013 Jun;38(6):273-274. PubMed PMID: 23538173. (Interview) Full Text
  - Richardson JS, Richardson DC. Studying and polishing the PDB's macromolecules. Biopolymers. 2013 Mar;99(3):170-182. PubMed PMID: 23023928. (Review) Full Text Link to Item
  - Richardson JS, Richardson DC. Invited review: Studying and polishing the PDB's macromolecules. Biopolymers. 2013 Mar 1;99(3):170-182. (Review) Full Text
  - Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics. 2013 Jan;42:265-287. PubMed Central PMCID: 23451892. (Review) Full Text
  - Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen C-Y, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods in Enzymology. 2013 Jan;523:87-107. PubMed Central PMCID: 23422427. Full Text
  - 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. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 2013 Jan;523:109-143. PubMed Central PMCID: 23422428. Full Text
  - Richardson JS, Prisant MG, Richardson DC. Crystallographic model validation: From diagnosis to healing. Current Opinion in Structural Biology. 2013;23(5):707-714. Full Text
  - Richardson JS, Richardson DC. Doing molecular biophysics: finding, naming, and picturing signal within complexity. Annu Rev Biophys. 2013;42:1-28. PubMed PMID: 23451888. Full Text Link to Item
  - Richardson JS, Richardson DC. The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest!. NATO Science for Peace and Security Series A: Chemistry and Biology. 2013:1-10. Full Text
  - 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. Graphical tools for macromolecular crystallography in PHENIX. Journal of Applied Crystallography. 2012 Jun;45(Pt 3):581-586. PubMed Central PMCID: 22675231. Full Text
  - Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica. Section D, Biological Crystallography. 2012 Apr;68(Pt 4):381-390. PubMed Central PMCID: 22505258. Full Text
  - Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. Plos Computational Biology. 2012 Jan;8(8):e1002629-null. PubMed Central PMCID: 22876172. Full Text
  - Richardson JS, Keedy DA, Richardson DC. “The plot” thickens: More data, more dimensions, more uses. 2012 Jan 1:46-61. (Chapter) Full Text
  - Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. A new generation of crystallographic validation tools for the protein data bank. Structure (London, England : 1993). 2011 Oct;19(10):1395-1412. PubMed Central PMCID: 22000512. Full Text
  - Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung L-W, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. The Phenix software for automated determination of macromolecular structures. Methods (San Diego, Calif.). 2011 Sep;55(1):94-106. PubMed Central PMCID: 21821126. Full Text
  - Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, Zirbel CL, Leontis NB. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Applied Ontology. 2011 Aug 31;6(1):53-89. Full Text
  - Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JHD. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science (New York, N.Y.). 2011 May;332(6032):981-984. PubMed Central PMCID: 21596992. Full Text
  - Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology. 2011 Jan;405(2):607-618. PubMed Central PMCID: 21073878. Full Text
  - Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Journal of Applied Crystallography. 2010 Aug;43(Pt 4):669-676. PubMed Central PMCID: 20648263. Full Text
  - Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica. Section D, Biological Crystallography. 2010 Feb;66(Pt 2):213-221. PubMed Central PMCID: 20124702. Full Text
  - Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography. 2010 Jan;66(Pt 1):12-21. PubMed Central PMCID: 20057044. Full Text
  - Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. J Struct Funct Genomics. 2009 Mar;10(1):83-93. PubMed PMID: 19002604. Full Text Link to Item
  - Block JN, Zielinski DJ, Chen VB, Davis IW, Vinson EC, Brady R, Richardson JS, Richardson DC. KinImmerse: Macromolecular VR for NMR ensembles. Source code for biology and medicine. 2009 Feb 17;4:3-. PubMed PMID: 19222844. Full Text
  - Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC. Recent developments in phasing and structure refinement for macromolecular crystallography. Current Opinion in Structural Biology. 2009;19(5):566-572. PubMed PMID: 19700309. Full Text
  - Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins. 2009;77 Suppl 9:29-49. PubMed PMID: 19731372. Full Text Link to Item
  - Tress ML, Ezkurdia I, Richardson JS. Target domain definition and classification in CASP8. Proteins. 2009 Jan;77 Suppl 9:10-17. PubMed Central PMCID: 19603487. Full Text
  - Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Algorithm for backrub motions in protein design. Bioinformatics (Oxford, England). 2008 Jul;24(13):i196-i204. PubMed Central PMCID: 18586714. Full Text
  - 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 . RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). Rna (New York, N.Y.). 2008 Mar;14(3):465-481. PubMed Central PMCID: 18192612. Full Text
  - Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. Journal of Mathematical Biology. 2008 Jan;56(1-2):253-278. PubMed Central PMCID: 17401565. Full Text
  - Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research. 2007 Jul;35(Web Server issue):W375-W383. PubMed Central PMCID: 17452350. Full Text
  - Kelley L-LC, Dillard BD, Tempel W, Chen L, Shaw N, Lee D, Newton MG, Sugar FJ, Jenney FE, Lee HS, Shah C, Poole FL, Adams MWW, Richardson JS, Richardson DC, Liu Z-J, Wang B-C, Rose J. Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 2007 Jul;63(Pt 7):549-552. PubMed Central PMCID: 17620707. Full Text
  - Gerwe B, Kelley L-LC, Dillard BD, Lai T, Liu Z-J, Tempel W, Chen L, Habel J, Lee D, Jr FEJ, Sugar FJ, Richardson JS, Richardson DC, Newton MG, Wang B-C, Adams MWW, Rose JP. Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: A component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon. Journal of Structural and Functional Genomics. 2007;8(1):1-10. PubMed PMID: 17932790. Full Text
  - Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 2006 Apr;12(4):533-541. PubMed Central PMCID: 16484377. (Letter) Full Text
  - Davis IW, Arendall WB, Richardson DC, Richardson JS. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure (London, England : 1993). 2006 Feb;14(2):265-274. PubMed Central PMCID: 16472746. Full Text
  - Richardson J. Vis capstone address: Designing visualizations to enable molecular insights. IEEE Transactions on Visualization and Computer Graphics. 2006;12(5):xxvi-.
  - Xu H, Yang C, Chen L, Kataeva IA, Tempel W, Lee D, Habel JE, Nguyen D, Pflugrath JW, Ferrara JD, Arendall WB, Richardson JS, Richardson DC, Liu ZJ, Newton MG, Rose JP, Wang BC. Away from the edge II: in-house Se-SAS phasing with chromium radiation. Acta Crystallographica Section D: Biological Crystallography. 2005 Jul;61(Pt 7):960-966. PubMed Central PMCID: 15983419. Full Text
  - Liu Z-J, Tempel W, Ng JD, Lin D, Shah AK, Chen L, Horanyi PS, Habel JE, Kataeva IA, Xu H, Yang H, Chang JC, Huang L, Chang S-H, Zhou W, Lee D, Praissman JL, Zhang H, Newton MG, Rose JP, Richardson JS, Richardson DC, Wang B-C. The high-throughput protein-to-structure pipeline at SECSG. Acta Crystallographica Section D: Biological Crystallography. 2005 Jun;61(Pt 6):679-684. PubMed Central PMCID: 15930619. Full Text
  - Murray LJW, Richardson JS, Arendall WB, Richardson DC. RNA backbone rotamers--finding your way in seven dimensions. Biochem Soc Trans. 2005 Jun;33(Pt 3):485-487. PubMed PMID: 15916548. Full Text Link to Item
  - Arendall WB, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, Liu Z-J, Rose JP, Carson WM, Luo M, Richardson DC, Wang B-C. A test of enhancing model accuracy in high-throughput crystallography. Journal of Structural and Functional Genomics. 2005 Jan;6(1):1-11. PubMed Central PMCID: 15965733. Full Text
  - Booth D, Jr RCB, Sirochman R, Richardson DC, Richardson JS, Weiner SW, Farwell M, Putnam-Evans C. Assessment of molecular construction in undergraduate biochemistry. Journal of Chemical Education. 2005;82(12):1854-1858.
  - Butterfoss GL, Richardson JS, Hermans J. Protein imperfections: separating intrinsic from extrinsic variation of torsion angles. Acta Crystallographica Section D: Biological Crystallography. 2005 Jan;61(Pt 1):88-98. PubMed Central PMCID: 15608380. Full Text
  - Tempel W, Liu Z-J, Schubot FD, Shah A, Weinberg MV, Jenney FE, Arendall WB, Adams MWW, Richardson JS, Richardson DC, Rose JP, Wang B-C. Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. Proteins. 2004 Dec;57(4):878-882. PubMed Central PMCID: 15468318. Full Text
  - Videau LL, Arendall WB, Richardson JS. The cis-Pro touch-turn: a rare motif preferred at functional sites. Proteins. 2004 Aug;56(2):298-309. PubMed Central PMCID: 15211513. Full Text
  - Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Research. 2004 Jul;32(Web Server issue):W615-W619. PubMed Central PMCID: 15215462. Full Text
  - Wales TE, Richardson JS, Fitzgerald MC. Facile chemical synthesis and equilibrium unfolding properties of CopG. Protein Science : a Publication of the Protein Society. 2004 Jul;13(7):1918-1926. PubMed Central PMCID: 15169951. Full Text
  - Kapp GT, Richardson JS, Oas TG. Kinetic role of helix caps in protein folding is context-dependent. Biochemistry. 2004 Apr 6;43(13):3814-3823. PubMed PMID: 15049688. Full Text Link to Item
  - Richardson JS. The protein surface is a moving target. Structure. 2004;12(6):912-913. PubMed PMID: 15274911. Full Text
  - Murray LJW, Arendall WB, Richardson DC, Richardson JS. RNA backbone is rotameric. Proceedings of the National Academy of Sciences of the United States of America. 2003 Nov 11;100(24):13904-13909. PubMed Central PMCID: 14612579. Full Text
  - Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb;50(3):437-450. PubMed Central PMCID: 12557186. Full Text
  - Richardson JS, Bryan WA, Richardson DC. New tools and data for improving structures, using all-atom contacts. Methods in Enzymology. 2003 Jan;374:385-412. PubMed Central PMCID: 14696383. Full Text
  - Richardson JS. All-atom contacts: a new approach to structure validation. Methods Biochem Anal. 2003;44:305-320. PubMed PMID: 12647392. Link to Item
  - Richardson JS, Richardson DC. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proceedings of the National Academy of Sciences of the United States of America. 2002 Mar;99(5):2754-2759. PubMed Central PMCID: 11880627. Full Text
  - Jr RCB, Booth D, Sirochman R, Richardson J, Richardson D. Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry. Journal of Chemical Education. 2002;79(5):551--.
  - Richardson DC, Richardson JS. Teaching molecular 3-D literacy. Biochemistry and Molecular Biology Education. 2002;30(1):21-26. Full Text
  - Grell D, Richardson JS, Mutter M. Protein design and folding: template trapping of self-assembled helical bundles. J Pept Sci. 2001 Mar;7(3):146-151. PubMed PMID: 11297350. Full Text Link to Item
  - Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins. 2000 Aug;40(3):389-408. PubMed Central PMCID: 10861930. Full Text
  - Richardson JS. Early ribbon drawings of proteins. Nat Struct Biol. 2000 Aug;7(8):624-625. PubMed PMID: 10932243. Full Text Link to Item
  - Grell D, Richardson JS, Richardson DC, Mutter M. SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics. J Mol Graph Model. 2000 Jun;18(3):290-310. PubMed PMID: 11021545. Link to Item
  - Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):400-405. PubMed PMID: 9892645. Link to Item
  - Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Journal of Molecular Biology. 1999 Jan;285(4):1711-1733. PubMed Central PMCID: 9917407. Full Text
  - Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Journal of Molecular Biology. 1999 Jan;285(4):1735-1747. PubMed Central PMCID: 9917408. Full Text
  - Ghaemmaghami S, Word JM, Burton RE, Richardson JS, Oas TG. Folding kinetics of a fluorescent variant of monomeric lambda repressor. Biochemistry. 1998 Jun;37(25):9179-9185. PubMed Central PMCID: 9636065. Full Text
  - Gernert KM, Thomas BD, Plurad JC, Richardson JS, Richardson DC, Bergman LD. Puzzle pieces defined: locating common packing units in tertiary protein contacts. Pac Symp Biocomput. 1996:331-349. PubMed PMID: 9390242. Link to Item
  - Gernert KM, Surles MC, Labean TH, Richardson JS, Richardson DC. The Alacoil: a very tight, antiparallel coiled-coil of helices. Protein Science : a Publication of the Protein Society. 1995 Nov;4(11):2252-2260. PubMed Central PMCID: 8563621. Full Text
  - Bergman LD, Richardson JS, Richardson DC. An algorithm for smoothly tessellating beta-sheet structures in proteins. J Mol Graph. 1995 Feb;13(1):36-58. PubMed PMID: 7794833. Link to Item
  - Richardson JS. Introduction: protein motifs. Faseb Journal : Official Publication of the Federation of American Societies for Experimental Biology. 1994 Dec;8(15):1237-1239. PubMed Central PMCID: 8001735. Full Text
  - Hemmingsen JM, Gernert KM, Richardson JS, Richardson DC. The tyrosine corner: a feature of most Greek key beta-barrel proteins. Protein Science : a Publication of the Protein Society. 1994 Nov;3(11):1927-1937. PubMed Central PMCID: 7703839. Full Text
  - Quinn TP, Tweedy NB, Williams RW, Richardson JS, Richardson DC. Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. Proceedings of the National Academy of Sciences of the United States of America. 1994 Sep;91(19):8747-8751. PubMed Central PMCID: 8090717. Full Text
  - Richardson DC, Richardson JS. Kinemages--simple macromolecular graphics for interactive teaching and publication. Trends Biochem Sci. 1994 Mar;19(3):135-138. PubMed PMID: 8203021. Link to Item
  - Surles MC, Richardson JS, Richardson DC, Brooks FP. Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system. Protein Sci. 1994 Feb;3(2):198-210. PubMed PMID: 8003957. (Review) Full Text Link to Item
  - Bergman LD, Richardson JS. VIEW-An exploratory molecular visualization system with user-definable interaction sequences. Proc ACM SIGGRAPH 93 Conf Comput Graphics. 1993:117-126.
  - Richardson JS, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, Hecht MH, Erickson BW, Yan Y, McClain RD, Donlan ME. Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophys J. 1992 Nov;63(5):1185-1209. PubMed PMID: 1477272. (Review) Link to Item
  - RICHARDSON JS, RICHARDSON DC. THE PROTEIN TOURIST - A NEW SERIES ON DISKETTE. PROTEIN SCIENCE. 1992 Mar;1(3):309-309. Link to Item
  - Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Science : a Publication of the Protein Society. 1992 Jan;1(1):3-9. PubMed Central PMCID: 1304880. Full Text
  - Frankel A, Welsh P, Richardson J, Robertus JD. Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes. Molecular and Cellular Biology. 1990 Dec;10(12):6257-6263. PubMed Central PMCID: 1978925. Full Text
  - Hecht MH, Richardson JS, Richardson DC, Ogden RC. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science. 1990 Aug 24;249(4971):884-891. PubMed PMID: 2392678. Link to Item
  - Richardson JS, Richardson DC. The de novo design of protein structures. Trends Biochem Sci. 1989 Jul;14(7):304-309. PubMed PMID: 2672455. (Review) Link to Item
  - Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science (New York, N.Y.). 1988 Jun;240(4859):1648-1652. PubMed Central PMCID: 3381086. Full Text
  - Richardson JS, Richardson DC. Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal. Proteins. 1988;4(4):229-239. PubMed PMID: 2855370. Full Text Link to Item
  - McRee DE, Richardson DC, Richardson JS, Siegel LM. The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase. J Biol Chem. 1986 Aug 5;261(22):10277-10281. PubMed PMID: 3525540. Link to Item
  - DANIELS SB, BOBE FW, REDDY PA, RICHARDSON JS, RICHARDSON DC, ERICKSON BW. PROTEIN ENGINEERING THROUGH CHEMICAL SYNTHESIS - DESIGN AND SYNTHESIS OF BETABELLIN-4 AND BETABELLIN-5. FEDERATION PROCEEDINGS. 1986 May;45(6):1788-1788. Link to Item
  - McRee DE, Richardson DC, Richardson JS, Siegel LM. The heme and Fe4S4cluster in the crystallographic structure of Escherichia coli sulfite reductase. Journal of Biological Chemistry. 1986 Jan 1;261(22):10277-10281.
  - Murata M, Richardson JS, Sussman JL. Simultaneous comparison of three protein sequences. Proceedings of the National Academy of Sciences of the United States of America. 1985 May;82(10):3073-3077. PubMed Central PMCID: 3858804. Full Text
  - McRee DE, Richardson JS, Richardson DC. Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli. J Mol Biol. 1985 Apr 5;182(3):467-468. PubMed PMID: 3892013. Link to Item
  - DANIELS SB, UNSON CG, RICHARDSON JS, RICHARDSON DC, ERICKSON BW. PROTEIN ENGINEERING THROUGH CHEMICAL SYNTHESIS - DESIGN AND SYNTHESIS OF BETABELLIN-2. FEDERATION PROCEEDINGS. 1985;44(3):694-694. Link to Item
  - Daniels SB, Unson CG, Richardson JS. Protein engineering through chemical synthesis: Design and synthesis of betabellin 2. Federation Proceedings. 1985;44(3):No.-1659.
  - Richardson JS, Richardson DC. Interpretation of electron density maps. Methods Enzymol. 1985;115:189-206. PubMed PMID: 3841180. Link to Item
  - Richardson JS. Schematic drawings of protein structures. Methods Enzymol. 1985;115:359-380. PubMed PMID: 3853075. Link to Item
  - Richardson JS. Describing patterns of protein tertiary structure. Methods Enzymol. 1985;115:341-358. PubMed PMID: 4079792. Link to Item
  - Richardson JS. Protein structure: A new twist for hairpin turns. Nature. 1985;316(6024):102-103. Full Text
  - RICHARDSON JS, RICHARDSON DC, ERICKSON BW. DENOVO DESIGN AND SYNTHESIS OF A PROTEIN. BIOPHYSICAL JOURNAL. 1984;45(2):A25-A25. Link to Item
  - Getzoff ED, Tainer JA, Weiner PK, Kollman PA, Richardson JS, Richardson DC. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature. 1983 Nov;306(5940):287-290. PubMed Central PMCID: 6646211. Full Text
  - Tainer JA, Getzoff ED, Richardson JS, Richardson DC. Structure and mechanism of copper, zinc superoxide dismutase. Nature. 1983 Nov;306(5940):284-287. PubMed Central PMCID: 6316150. Full Text
  - Tainer JA, Getzoff ED, Beem KM, Richardson JS, Richardson DC. Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. Journal of Molecular Biology. 1982 Sep;160(2):181-217. PubMed Central PMCID: 7175933. Full Text
  - Taylor HC, Richardson DC, Richardson JS, Wlodawer A, Komoriya A, Chaikes IM. "Active" conformation of an inactive semi-synthetic ribonuclease-S. Journal of Molecular Biology. 1981 Jun;149(2):313-317. PubMed Central PMCID: 7310884. Full Text
  - Richardson JS. The anatomy and taxonomy of protein structure. Advances in Protein Chemistry. 1981 Jan;34:167-339. PubMed Central PMCID: 7020376. (Review)
  - Drenth J, Low BW, Richardson JS, Wright CS. The toxin-agglutinin fold. A new group of small protein structures organized around a four-disulfide core. J Biol Chem. 1980 Apr 10;255(7):2652-2655. PubMed PMID: 6892639. Link to Item
  - GETZOFF ED, TAINER JA, SACK JS, BICKAR D, RICHARDSON JS, RICHARDSON DC. CRYSTALLOGRAPHIC STUDIES OF A ROOT EFFECT HEMOGLOBIN. FEDERATION PROCEEDINGS. 1980;39(6):2192-2192. Link to Item
  - RICHARDSON JS, TAINER JA, RICHARDSON DC. AN ILLUSTRATED MUSEUM OF PROTEIN STRUCTURES. BIOPHYSICAL JOURNAL. 1980;32(1):211-213. PubMed PMID: 19431356. Full Text Link to Item
  - Richardson JS. The singly-wound parallel beta barrel: a proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase. Biochem Biophys Res Commun. 1979 Sep 12;90(1):285-290. PubMed PMID: 496979. Link to Item
  - Kimball MR, Sato A, Richardson JS, Rosen LS, Low BW. Molecular conformation of erabutoxin b; atomic coordinates at 2.5 A resolution. Biochem Biophys Res Commun. 1979 Jun 13;88(3):950-959. PubMed PMID: 465091. Link to Item
  - TAINER JA, GETZOFF ED, RICHARDSON JS, RICHARDSON DC. PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDY OF A ROOT EFFECT HEMOGLOBIN. BIOPHYSICAL JOURNAL. 1979;25(2):A40-A40. Link to Item
  - Richardson JS, Getzoff ED, Richardson DC. The beta bulge: a common small unit of nonrepetitive protein structure. Proceedings of the National Academy of Sciences of the United States of America. 1978 Jun;75(6):2574-2578. PubMed Central PMCID: 275827. Full Text
  - Richardson JS. beta-Sheet topology and the relatedness of proteins. Nature. 1977 Aug;268(5620):495-500. PubMed Central PMCID: 329147. (Review) Full Text
  - Low BW, Preston HS, Sato A, Rosen LS, Searl JE, Rudko AD, Richardson JS. Three dimensional structure of erabutoxin b neurotoxic protein: inhibitor of acetylcholine receptor. Proc Natl Acad Sci U S A. 1976 Sep;73(9):2991-2994. PubMed PMID: 1067597. Link to Item
  - Beem KM, Richardson JS, Richardson DC. Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies. J Mol Biol. 1976 Aug 5;105(2):327-332. PubMed PMID: 787536. Link to Item
  - Richardson JS. Handedness of crossover connections in beta sheets. Proceedings of the National Academy of Sciences of the United States of America. 1976 Aug;73(8):2619-2623. PubMed Central PMCID: 183204. Full Text
  - Richardson JS, Richardson DC, Thomas KA, Silverton EW, Davies DR. Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit. J Mol Biol. 1976 Apr 5;102(2):221-235. PubMed PMID: 1271464. Link to Item
  - Richardson JS, Thomas KA, Richardson DC. Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase. Biochem Biophys Res Commun. 1975 Apr 21;63(4):986-992. PubMed PMID: 1169067. Link to Item
  - Richardson J, Thomas KA, Rubin BH, Richardson DC. Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands. Proc Natl Acad Sci U S A. 1975 Apr;72(4):1349-1353. PubMed PMID: 1055410. Link to Item
  - Thomas KA, Rubin BH, Bier CJ, Richardson JS, Richardson DC. The crystal structure of bovine Cu2+,Zn2+ superoxide dismutase at 5.5-A resolution. J Biol Chem. 1974 Sep 10;249(17):5677-5683. PubMed PMID: 4472353. Link to Item
  - Richardson DC, Bier CJ, Richardson JS. Two crystal forms of bovine superoxide dismutase. J Biol Chem. 1972 Oct 10;247(19):6368-6369. PubMed PMID: 4675640. Link to Item
  - Rubin B, Richardson JS. The simple construction of protein alpha-carbon models. Biopolymers. 1972;11(11):2381-2385. PubMed PMID: 4634874. Full Text Link to Item
  - Arnone A, Bier CJ, Cotton FA, Day VW, Hazen EE, Richardson DC, Yonath A, Richardson JS. A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing. J Biol Chem. 1971 Apr 10;246(7):2302-2316. PubMed PMID: 5555571. Link to Item
  - Arnone A, Bier CJ, Cotton FA, Hazen EE, Richardson DC, Richardson JS. The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution. Proc Natl Acad Sci U S A. 1969 Oct;64(2):420-427. PubMed PMID: 5261023. Link to Item
  - Lewis DK, Richardson JS. Scriven on human unpredictability. Philosophical Studies. 1966;17(5):69-74. Full Text
- Book Sections
  - Richardson JS. All-Atom Contacts: A New Approach to Structure Validation. In: Structural Bioinformatics. 2005 Jan 28. p. 305-320. Full Text
- Reports
  - Leduc JW, Baric R, Breeze RG, Buller RM, Eddy SR, Falkow S, Levinson RE, Mulligan J, O'Brien AD, Ochoa-Corona F, Richardson JS, Riley M, Slezak T. Sequence-Based Classification of Select Agents: A Brighter Line. National Academies Press; 2010. Open Access Copy Link to Item
- Conference Papers
  - Bergman LD, Richardson JS. VIEW-An exploratory molecular visualization system with user-definable interaction sequences. 1993 Dec 1:117-126.
Exhibitions, Screenings, & Performances
- Ribbon drawing of triose phosphate isomerase 3D protein structure | Picture of The Day at English Wikipedia 2009
Artistic Works & Non-Print Media
- Drawings
  - Ribbon drawing of triose phosphate isomerase 3D protein structure. Visual artist. 1981
Teaching & Mentoring
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