Jane Shelby Richardson | Scholars@Duke

Jane Shelby Richardson
James B. Duke Distinguished 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 Distinguished 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
Lab Website
MolProbity Validation

Background
Education, Training, & Certifications
- M.A., Harvard University 1966
Recognition
In the News
- MAR 15, 2021 Medical Center Archives
  
  Women of Duke Health
- 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
- Extending MolProbity Diagnosis & Healing Methods to Empower Better CryoEM & Xray Models at 2.5-4A Resolution, plus Versioned, Redeposited "GEMS" for Important Individual Structures awarded by National Institutes of Health 2019 - 2024
- PHENIX: New methods for automation in macromolecular crystallography awarded by Ernest Orlando Lawrence Berkeley National Laboratory 2006 - 2023
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Organization and Function of Cellular Structure awarded by National Institutes of Health 1975 - 2020
- MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine awarded by National Institutes of Health 2015 - 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
- same awarded by National Institutes of Health 1999 - 2005
- Analysis and Design of Protein Structures awarded by National Institutes of Health 1984 - 2004
- Same 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
External Relationships
- Ten63 Therapeutics
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Williams CJ, Richardson DC, Richardson JS. The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. Protein Sci. 2022 Jan;31(1):290–300.
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  - Croll TI, Diederichs K, Fischer F, Fyfe CD, Gao Y, Horrell S, et al. Making the invisible enemy visible. Nat Struct Mol Biol. 2021 May;28(5):404–8.
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  - Croll TI, Williams CJ, Chen VB, Richardson DC, Richardson JS. Improving SARS-CoV-2 structures: Peer review by early coordinate release. Biophys J. 2021 Mar 16;120(6):1085–96.
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  - Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, et al. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods. 2021 Feb;18(2):156–64.
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  - Richardson JS, Richardson DC, Goodsell DS. Seeing the PDB. J Biol Chem. 2021 Jan;296:100742.
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  - Croll T, Diederichs K, Fischer F, Fyfe C, Gao Y, Horrell S, et al. Making the invisible enemy visible. Biorxiv. 2020 Dec 28;
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  - Richardson JS. A new way to see RNAs. Nat Methods. 2020 Jul;17(7):663–4.
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  - Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, et al. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Crystallogr D Struct Biol. 2020 Jan 1;76(Pt 1):51–62.
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  - Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC. New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. Protein Sci. 2020 Jan;29(1):315–29.
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  - Prisant M, Williams C, Chen V, Richardson J, Richardson D. CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation. 2019 Oct 7;
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  - Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861–77.
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  - 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. J Struct Biol. 2018 Nov;204(2):301–12.
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  - Wang Y, Shekhar M, Thifault D, Williams CJ, McGreevy R, Richardson J, et al. Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons. J Struct Biol. 2018 Nov;204(2):319–28.
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  - Richardson JS, Williams CJ, Hintze BJ, Chen VB, Prisant MG, Videau LL, et al. Model validation: local diagnosis, correction and when to quit. Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):132–42.
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  - Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018 Jan;27(1):293–315.
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  - Hintze BJ, Richardson JS, Richardson DC. Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallogr D Struct Biol. 2017 Oct 1;73(Pt 10):852–9.
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  - 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. J Mol Biol. 2017 May 5;429(9):1321–35.
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  - Hintze BJ, Lewis SM, Richardson JS, Richardson DC. Molprobity's ultimate rotamer-library distributions for model validation. Proteins. 2016 Sep;84(9):1177–89.
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  - Hintze BJ, Lewis SM, Richardson JS, Richardson DC. Cover Image, Volume 84, Issue 9. Proteins: Structure, Function and Bioinformatics. 2016 Sep 1;84(9):C1.
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  - Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, et al. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res. 2015 Apr 20;43(7):3420–33.
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  - Jain S, Richardson DC, Richardson JS. Computational Methods for RNA Structure Validation and Improvement. Methods Enzymol. 2015;558:181–212.
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  - 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 Res. 2014 Nov 10;42(20):12833–46.
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  - Deis LN, Pemble CW, Qi Y, Hagarman A, Richardson DC, Richardson JS, et al. Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Structure. 2014 Oct 7;22(10):1467–77.
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  - Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, et al. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1104–14.
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  - Richardson JS, Richardson DC. Biophysical highlights from 54 years of macromolecular crystallography. Biophys J. 2014 Feb 4;106(3):510–25.
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  - Richardson JS, Prisant MG, Richardson DC. Crystallographic model validation: from diagnosis to healing. Curr Opin Struct Biol. 2013 Oct;23(5):707–14.
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  - Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, et al. Recommendations of the wwPDB NMR Validation Task Force. Structure. 2013 Sep 3;21(9):1563–70.
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  - Richardson J. An interview with Jane Richardson. Trends Biochem Sci. 2013 Jun;38(6):273–4.
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  - Richardson JS, Richardson DC. Studying and polishing the PDB's macromolecules. Biopolymers. 2013 Mar;99(3):170–82.
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  - Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, et al. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annu Rev Biophys. 2013;42:265–87.
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  - Leaver-Fay A, O’Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol. 2013;523:109–43.
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  - Richardson JS, Richardson DC. Doing molecular biophysics: finding, naming, and picturing signal within complexity. Annu Rev Biophys. 2013;42:1–28.
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  - 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 Jan 1;1–10.
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  - Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen C-Y, et al. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods Enzymol. 2013;523:87–107.
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  - Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, et al. Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581–6.
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  - Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, et al. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):381–90.
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  - Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. Plos Comput Biol. 2012;8(8):e1002629.
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  - Richardson JS, Keedy DA, Richardson DC. “The plot” thickens: More data, more dimensions, more uses. 2012 Jan 1;46–61.
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  - Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, et al. A new generation of crystallographic validation tools for the protein data bank. Structure. 2011 Oct 12;19(10):1395–412.
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  - Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, et al. The Phenix software for automated determination of macromolecular structures. Methods. 2011 Sep;55(1):94–106.
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  - Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, et al. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Applied Ontology. 2011 Aug 31;6(1):53–89.
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  - Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, et al. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science. 2011 May 20;332(6032):981–4.
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  - Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, et al. Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol. 2011 Jan 14;405(2):607–18.
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  - Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, et al. 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):669–76.
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  - Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213–21.
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  - Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12–21.
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  - Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, et al. Recent developments in phasing and structure refinement for macromolecular crystallography. Curr Opin Struct Biol. 2009 Oct;19(5):566–72.
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  - 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.
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  - Block JN, Zielinski DJ, Chen VB, Davis IW, Vinson EC, Brady R, et al. KinImmerse: Macromolecular VR for NMR ensembles. Source Code Biol Med. 2009 Feb 17;4:3.
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  - Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, et al. 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.
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  - Tress ML, Ezkurdia I, Richardson JS. Target domain definition and classification in CASP8. Proteins. 2009;77 Suppl 9:10–7.
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  - Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Algorithm for backrub motions in protein design. Bioinformatics. 2008 Jul 1;24(13):i196–204.
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  - Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, et al. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). Rna. 2008 Mar;14(3):465–81.
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  - Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. J Math Biol. 2008 Jan;56(1–2):253–78.
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  - Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375–83.
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  - Kelley L-LC, Dillard BD, Tempel W, Chen L, Shaw N, Lee D, et al. Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jul 1;63(Pt 7):549–52.
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  - Gerwe B, Kelley L-LC, Dillard BD, Lai T, Liu Z-J, Tempel W, et al. 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. J Struct Funct Genomics. 2007 Mar;8(1):1–10.
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  - Richardson J. Vis capstone address: Designing visualizations to enable molecular insights. Ieee Transactions on Visualization and Computer Graphics. 2006 Sep 1;12(5).
  - Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, et al. The RNA Ontology Consortium: an open invitation to the RNA community. Rna. 2006 Apr;12(4):533–41.
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  - Davis IW, Arendall WB, Richardson DC, Richardson JS. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure. 2006 Feb;14(2):265–74.
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  - Xu H, Yang C, Chen L, Kataeva IA, Tempel W, Lee D, et al. Away from the edge II: in-house Se-SAS phasing with chromium radiation. Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):960–6.
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  - Liu Z-J, Tempel W, Ng JD, Lin D, Shah AK, Chen L, et al. The high-throughput protein-to-structure pipeline at SECSG. Acta Crystallogr D Biol Crystallogr. 2005 Jun;61(Pt 6):679–84.
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  - 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):485–7.
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  - Arendall WB, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, et al. A test of enhancing model accuracy in high-throughput crystallography. J Struct Funct Genomics. 2005;6(1):1–11.
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  - Booth D, Bateman RC, Sirochman R, Richardson DC, Richardson JS, Weiner SW, et al. Assessment of molecular construction in undergraduate biochemistry. Journal of Chemical Education. 2005 Jan 1;82(12):1854–8.
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  - Butterfoss GL, Richardson JS, Hermans J. Protein imperfections: separating intrinsic from extrinsic variation of torsion angles. Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):88–98.
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  - Tempel W, Liu Z-J, Schubot FD, Shah A, Weinberg MV, Jenney FE, et al. Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. Proteins. 2004 Dec 1;57(4):878–82.
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  - Videau LL, Arendall WB, Richardson JS. The cis-Pro touch-turn: a rare motif preferred at functional sites. Proteins. 2004 Aug 1;56(2):298–309.
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  - Wales TE, Richardson JS, Fitzgerald MC. Facile chemical synthesis and equilibrium unfolding properties of CopG. Protein Sci. 2004 Jul;13(7):1918–26.
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  - Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W615–9.
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  - Richardson JS. The protein surface is a moving target. Structure. 2004 Jun;12(6):912–3.
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  - Kapp GT, Richardson JS, Oas TG. Kinetic role of helix caps in protein folding is context-dependent. Biochemistry. 2004 Apr 6;43(13):3814–23.
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  - Murray LJW, Arendall WB, Richardson DC, Richardson JS. RNA backbone is rotameric. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13904–9.
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  - Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb 15;50(3):437–50.
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  - Richardson JS, Bryan WA, Richardson DC. New tools and data for improving structures, using all-atom contacts. Methods Enzymol. 2003;374:385–412.
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  - Richardson JS. All-atom contacts: a new approach to structure validation. Methods Biochem Anal. 2003;44:305–20.
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  - Richardson JS, Richardson DC. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2754–9.
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  - Bateman RC, Booth D, Sirochman R, Richardson J, Richardson D. Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry. Journal of Chemical Education. 2002 Jan 1;79(5):551.
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  - Richardson DC, Richardson JS. Teaching molecular 3-D literacy. Biochemistry and Molecular Biology Education. 2002 Jan 1;30(1):21–6.
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  - Grell D, Richardson JS, Mutter M. Protein design and folding: template trapping of self-assembled helical bundles. J Pept Sci. 2001 Mar;7(3):146–51.
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  - Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins. 2000 Aug 15;40(3):389–408.
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  - Richardson JS. Early ribbon drawings of proteins. Nat Struct Biol. 2000 Aug;7(8):624–5.
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  - 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.
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  - Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol. 1999 Jan 29;285(4):1711–33.
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  - Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol. 1999 Jan 29;285(4):1735–47.
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  - 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):400–5.
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  - Ghaemmaghami S, Word JM, Burton RE, Richardson JS, Oas TG. Folding kinetics of a fluorescent variant of monomeric lambda repressor. Biochemistry. 1998 Jun 23;37(25):9179–85.
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  - Neurath H. The Kinemage: A tool for scientific communication. Protein Science. 1996 Nov;5(11):2147–2147.
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  - 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;331–49.
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  - Gernert KM, Surles MC, Labean TH, Richardson JS, Richardson DC. The Alacoil: a very tight, antiparallel coiled-coil of helices. Protein Sci. 1995 Nov;4(11):2252–60.
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  - 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.
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  - Richardson JS. Introduction: protein motifs. Faseb J. 1994 Dec;8(15):1237–9.
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  - Hemmingsen JM, Gernert KM, Richardson JS, Richardson DC. The tyrosine corner: a feature of most Greek key beta-barrel proteins. Protein Sci. 1994 Nov;3(11):1927–37.
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  - Quinn TP, Tweedy NB, Williams RW, Richardson JS, Richardson DC. Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. Proc Natl Acad Sci U S A. 1994 Sep 13;91(19):8747–51.
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  - Richardson DC, Richardson JS. Kinemages--simple macromolecular graphics for interactive teaching and publication. Trends Biochem Sci. 1994 Mar;19(3):135–8.
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  - 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.
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  - Bergman LD, Richardson JS, Richardson DC, Brooks FP. VIEW an exploratory molecular visualization system with user-definable interaction sequences. Proceedings of the 20th Annual Conference on Computer Graphics and Interactive Techniques, Siggraph 1993. 1993 Sep 1;117–26.
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  - Richardson JS, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, Hecht MH, et al. Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophys J. 1992 Nov;63(5):1185–209.
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  - RICHARDSON JS, RICHARDSON DC. THE PROTEIN TOURIST - A NEW SERIES ON DISKETTE. Protein Science. 1992 Mar 1;1(3):309–309.
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  - Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Sci. 1992 Jan;1(1):3–9.
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  - 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. Mol Cell Biol. 1990 Dec;10(12):6257–63.
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  - 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):884–91.
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  - Richardson JS, Richardson DC. The de novo design of protein structures. Trends Biochem Sci. 1989 Jul;14(7):304–9.
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  - Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science. 1988 Jun 17;240(4859):1648–52.
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  - 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):229–39.
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  - 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):10277–81.
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  - 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.
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  - McRee DE, Richardson DC, Richardson JS, Siegel LM. The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase. Journal of Biological Chemistry. 1986 Jan 1;261(22):10277–81.
  - Richardson JS. Protein structure: A new twist for hairpin turns. Nature. 1985 Dec 1;316(6024):102–3.
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  - Murata M, Richardson JS, Sussman JL. Simultaneous comparison of three protein sequences. Proc Natl Acad Sci U S A. 1985 May;82(10):3073–7.
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  - 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):467–8.
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  - DANIELS SB, UNSON CG, RICHARDSON JS, RICHARDSON DC, ERICKSON BW. PROTEIN ENGINEERING THROUGH CHEMICAL SYNTHESIS - DESIGN AND SYNTHESIS OF BETABELLIN-2. Federation Proceedings. 1985 Jan 1;44(3):694–694.
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  - Daniels SB, Unson CG, Richardson JS. Protein engineering through chemical synthesis: Design and synthesis of betabellin 2. Federation Proceedings. 1985 Jan 1;44(3).
  - Richardson JS, Richardson DC. Interpretation of electron density maps. Methods Enzymol. 1985;115:189–206.
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  - Richardson JS. Schematic drawings of protein structures. Methods Enzymol. 1985;115:359–80.
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  - Richardson JS. Describing patterns of protein tertiary structure. Methods Enzymol. 1985;115:341–58.
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  - RICHARDSON JS, RICHARDSON DC, ERICKSON BW. DENOVO DESIGN AND SYNTHESIS OF A PROTEIN. Biophysical Journal. 1984;45(2):A25–A25.
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  - Getzoff ED, Tainer JA, Weiner PK, Kollman PA, Richardson JS, Richardson DC. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature. 1983 Nov 17;306(5940):287–90.
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  - Tainer JA, Getzoff ED, Richardson JS, Richardson DC. Structure and mechanism of copper, zinc superoxide dismutase. Nature. 1983 Nov 17;306(5940):284–7.
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  - Tainer JA, Getzoff ED, Beem KM, Richardson JS, Richardson DC. Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. J Mol Biol. 1982 Sep 15;160(2):181–217.
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  - Taylor HC, Richardson DC, Richardson JS, Wlodawer A, Komoriya A, Chaikes IM. "Active" conformation of an inactive semi-synthetic ribonuclease-S. J Mol Biol. 1981 Jun 25;149(2):313–7.
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  - Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339.
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  - Richardson JS, Tainer JA, Richardson DC. An illustrated museum of protein structures. Biophys J. 1980 Oct;32(1):211–3.
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  - 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):2652–5.
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  - GETZOFF ED, TAINER JA, SACK JS, BICKAR D, RICHARDSON JS, RICHARDSON DC. CRYSTALLOGRAPHIC STUDIES OF A ROOT EFFECT HEMOGLOBIN. Federation Proceedings. 1980 Jan 1;39(6):2192–2192.
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  - 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):285–90.
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  - 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):950–9.
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  - TAINER JA, GETZOFF ED, RICHARDSON JS, RICHARDSON DC. PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDY OF A ROOT EFFECT HEMOGLOBIN. Biophysical Journal. 1979 Jan 1;25(2):A40–A40.
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  - Richardson JS, Getzoff ED, Richardson DC. The beta bulge: a common small unit of nonrepetitive protein structure. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2574–8.
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  - Richardson JS. beta-Sheet topology and the relatedness of proteins. Nature. 1977 Aug 11;268(5620):495–500.
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  - Low BW, Preston HS, Sato A, Rosen LS, Searl JE, Rudko AD, et al. Three dimensional structure of erabutoxin b neurotoxic protein: inhibitor of acetylcholine receptor. Proc Natl Acad Sci U S A. 1976 Sep;73(9):2991–4.
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  - 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):327–32.
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  - Richardson JS. Handedness of crossover connections in beta sheets. Proc Natl Acad Sci U S A. 1976 Aug;73(8):2619–23.
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  - 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):221–35.
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  - Richardson JS, Thomas KA, Richardson DC. Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase. Biochem Biophys Res Commun. 1975 Apr 21;63(4):986–92.
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  - 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):1349–53.
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  - 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):5677–83.
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  - Richardson DC, Bier CJ, Richardson JS. Two crystal forms of bovine superoxide dismutase. J Biol Chem. 1972 Oct 10;247(19):6368–9.
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  - Rubin B, Richardson JS. The simple construction of protein alpha-carbon models. Biopolymers. 1972;11(11):2381–5.
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  - Arnone A, Bier CJ, Cotton FA, Day VW, Hazen EE, Richardson DC, et al. 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):2302–16.
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  - 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):420–7.
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  - Lewis DK, Richardson JS. Scriven on human unpredictability. Philosophical Studies. 1966 Oct 1;17(5):69–74.
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- Book Sections
  - Richardson JS. All-Atom Contacts: A New Approach to Structure Validation. In: Structural Bioinformatics. 2005. p. 305–20.
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- Reports
  - Leduc JW, Baric R, Breeze RG, Buller RM, Eddy SR, Falkow S, et al. Sequence-Based Classification of Select Agents: A Brighter Line. National Academies Press; 2010.
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- Conference Papers
  - Williams C, Richardson DC, Richardson JS. A database of high-quality protein residues for reference data, library construction and motif analysis. In: Acta Crystallographica Section a Foundations and Advances. International Union of Crystallography (IUCr); 2019. p. a437–a437.
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  - Sarkar D, Vant J, Shekhar M, Richardson JS, Skeel R, Singharoy A. MDFF Error Analysis: A Tool for Determining Stereochemical and Thermodynamic Correct Structures. In: Biophysical Journal. Elsevier BV; 2019. p. 140a-141a.
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  - Richardson J, Richardson D. Physical Properties that Derive From, and Circle Back to Inform, 3D Protein Structure. In: Protein Science. WILEY-BLACKWELL; 2012. p. 64–64.
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  - Williams C, Richardson D, Richardson J. Clarity Through Squinting: C alpha-parameters for Accurate Backbone at Low Resolution. In: Protein Science. WILEY-BLACKWELL; 2012. p. 144–144.
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  - Echols N, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Headd JJ, et al. Graphical tools for structure determination and refinement inPHENIX. In: Acta Crystallographica Section a Foundations of Crystallography. International Union of Crystallography (IUCr); 2011. p. C161–2.
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  - Adams P, Afonine P, Echols N, Headd J, Grosse-Kunstleve R, Moriarty N. New tools for structure refinement inPHENIX. In: Acta Crystallographica Section a Foundations of Crystallography. International Union of Crystallography (IUCr); 2010. p. s15–s15.
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  - Grell D, Richardson JS, Richardson DC, Mutter M. Design of small symmetrical four-helix bundle proteins. In: Fields GB, Tam JP, Barany G, editors. Peptides for the New Millennium. SPRINGER; 2000. p. 293–4.
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  - Bergman LD, Richardson JS. VIEW-An exploratory molecular visualization system with user-definable interaction sequences. In: Proc Acm Siggraph 93 Conf Comput Graphics. 1993. p. 117–26.
  - MURATA M, RICHARDSON JS. SIMULTANEOUS COMPARISON OF 3 PROTEIN SEQUENCES. In: Proceedings of the Australian Biochemical Society. 1984. p. 47–47.
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- Preprints
  - Terwilliger T, Poon B, Afonine P, Schlicksup C, Croll T, Millán C, et al. Improved AlphaFold modeling with implicit experimental information. bioRxiv. 2022.
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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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