Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Massachusetts Institute of Technology 1968
• 

  Previous Appointments & Affiliations

  • Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 1969 - 2019
• Recognition
• 

  Awards & Honors

  • Distinguished Speaker, NC section of ACS. American Chemical Society. 2012
  • Gordon Hammes Teaching & Mentoring Award. Duke University. 2009
  • Amgen Award for Innovation in Protein Science. Protein Society. 1995
  • Special Achievement Award, BioTechnology Winter Symposium. BioTechnology. 1995
  • Science Digest 100 Best Innovations of 1985. Science Digest. 1985
• Expertise
• 

  Subject Headings

  • Biophysics
  • Computer Graphics
  • Crystallography, X-Ray
  • Databases, Nucleic Acid
  • Databases, Protein
  • Hepatitis Delta Virus
  • Hydrogen
  • Nucleic Acid Conformation
  • Protein Engineering
  • Protein Structure, Tertiary
  • RNA
  • RNA Cleavage
  • RNA, Catalytic
  • Software
  • Superoxide Dismutase
  • User-Computer Interface
  • X-Ray Diffraction
• 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
  • Automated detection of protein crystals in high-throughput crystallography experiments awarded by North Carolina Biotechnology Center 2014 - 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
  • Predoctoral Fellowship Awards for Students with Disabilities (F31) awarded by National Institutes of Health 2006 - 2009
  • 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
  • Molecular Biophysics Training Program awarded by National Institutes of Health 1994 - 1999
  • Molecular Biophysics Training Program awarded by National Institutes of Health 1994 - 1999
  • Molecular Biophysics Training Program awarded by National Institutes of Health 1994 - 1999
  • 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
  • Macromolecular Crystallography And Protein Chemistry awarded by National Aeronautics and Space Administration 1990 - 1991
  • Crystallographic Analysis Of Protein Structures awarded by National Institutes of Health 1987 - 1989
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Williams, Christopher J., David C. Richardson, and Jane S. Richardson. “The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues.” Protein Sci 31, no. 1 (January 2022): 290–300. https://doi.org/10.1002/pro.4239.
       Full Text  Link to Item
    • Croll, Tristan I., Christopher J. Williams, Vincent B. Chen, David C. Richardson, and Jane S. Richardson. “Improving SARS-CoV-2 structures: Peer review by early coordinate release.” Biophys J 120, no. 6 (March 16, 2021): 1085–96. https://doi.org/10.1016/j.bpj.2020.12.029.
       Full Text  Link to Item
    • Richardson, Jane S., David C. Richardson, and David S. Goodsell. “Seeing the PDB.” J Biol Chem 296 (2021): 100742. https://doi.org/10.1016/j.jbc.2021.100742.
       Full Text  Link to Item
    • Prisant, Michael G., Christopher J. Williams, Vincent B. Chen, Jane S. Richardson, and David C. Richardson. “New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.” Protein Sci 29, no. 1 (January 2020): 315–29. https://doi.org/10.1002/pro.3786.
       Full Text  Link to Item
    • Liebschner, Dorothee, Pavel V. Afonine, Matthew L. Baker, Gábor Bunkóczi, Vincent B. Chen, Tristan I. Croll, Bradley Hintze, et al. “Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.” Acta Crystallogr D Struct Biol 75, no. Pt 10 (October 1, 2019): 861–77. https://doi.org/10.1107/S2059798319011471.
       Full Text  Link to Item
    • Richardson, Jane S., Christopher J. Williams, Lizbeth L. Videau, Vincent B. Chen, and David C. Richardson. “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 204, no. 2 (November 2018): 301–12. https://doi.org/10.1016/j.jsb.2018.08.007.
       Full Text  Link to Item
    • Richardson, Jane S., Christopher J. Williams, Bradley J. Hintze, Vincent B. Chen, Michael G. Prisant, Lizbeth L. Videau, and David C. Richardson. “Model validation: local diagnosis, correction and when to quit.” Acta Crystallogr D Struct Biol 74, no. Pt 2 (February 1, 2018): 132–42. https://doi.org/10.1107/S2059798317009834.
       Full Text  Link to Item
    • Williams, Christopher J., Jeffrey J. Headd, Nigel W. Moriarty, Michael G. Prisant, Lizbeth L. Videau, Lindsay N. Deis, Vishal Verma, et al. “MolProbity: More and better reference data for improved all-atom structure validation.” Protein Sci 27, no. 1 (January 2018): 293–315. https://doi.org/10.1002/pro.3330.
       Full Text  Link to Item
    • Hintze, Bradley J., Jane S. Richardson, and David C. Richardson. “Mismodeled purines: implicit alternates and hidden Hoogsteens.” Acta Crystallogr D Struct Biol 73, no. Pt 10 (October 1, 2017): 852–59. https://doi.org/10.1107/S2059798317013729.
       Full Text  Link to Item
    • Zheng-Bradley, Xiangqun, Ian Streeter, Susan Fairley, David Richardson, Laura Clarke, Paul Flicek, and Paul 1000 Genomes Project Consortium. “Alignment of 1000 Genomes Project reads to reference assembly GRCh38.” Gigascience 6, no. 7 (July 1, 2017): 1–8. https://doi.org/10.1093/gigascience/gix038.
       Full Text  Link to Item
    • Richardson, Jane S., Lizbeth L. Videau, Christopher J. Williams, and David C. Richardson. “Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding.” J Mol Biol 429, no. 9 (May 5, 2017): 1321–35. https://doi.org/10.1016/j.jmb.2017.03.017.
       Full Text  Link to Item
    • Ecker, Simone, Lu Chen, Vera Pancaldi, Frederik O. Bagger, José María Fernández, Enrique Carrillo de Santa Pau, David Juan, et al. “Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.” Genome Biol 18, no. 1 (January 26, 2017): 18. https://doi.org/10.1186/s13059-017-1156-8.
       Full Text  Link to Item
    • Fernández, José María, Victor de la Torre, David Richardson, Romina Royo, Montserrat Puiggròs, Valentí Moncunill, Stamatina Fragkogianni, et al. “The BLUEPRINT Data Analysis Portal.” Cell Syst 3, no. 5 (November 23, 2016): 491-495.e5. https://doi.org/10.1016/j.cels.2016.10.021.
       Full Text  Link to Item
    • Chen, Lu, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, et al. “Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.” Cell 167, no. 5 (November 17, 2016): 1398-1414.e24. https://doi.org/10.1016/j.cell.2016.10.026.
       Full Text  Link to Item
    • Javierre, Biola M., Oliver S. Burren, Steven P. Wilder, Roman Kreuzhuber, Steven M. Hill, Sven Sewitz, Jonathan Cairns, et al. “Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.” Cell 167, no. 5 (November 17, 2016): 1369-1384.e19. https://doi.org/10.1016/j.cell.2016.09.037.
       Full Text  Link to Item
    • Stunnenberg, Hendrik G., Hendrik G. International Human Epigenome Consortium, and Martin Hirst. “The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.” Cell 167, no. 5 (November 17, 2016): 1145–49. https://doi.org/10.1016/j.cell.2016.11.007.
       Full Text  Link to Item
    • Hintze, B. J., S. M. Lewis, J. S. Richardson, and D. C. Richardson. “Cover Image, Volume 84, Issue 9.” Proteins: Structure, Function and Bioinformatics 84, no. 9 (September 1, 2016): C1. https://doi.org/10.1002/prot.25109.
       Full Text
    • Hintze, Bradley J., Steven M. Lewis, Jane S. Richardson, and David C. Richardson. “Molprobity's ultimate rotamer-library distributions for model validation.” Proteins 84, no. 9 (September 2016): 1177–89. https://doi.org/10.1002/prot.25039.
       Full Text  Link to Item
    • Kulis, Marta, Angelika Merkel, Simon Heath, Ana C. Queirós, Ronald P. Schuyler, Giancarlo Castellano, Renée Beekman, et al. “Whole-genome fingerprint of the DNA methylome during human B cell differentiation.” Nat Genet 47, no. 7 (July 2015): 746–56. https://doi.org/10.1038/ng.3291.
       Full Text  Link to Item
    • Agirre, Xabier, Giancarlo Castellano, Marien Pascual, Simon Heath, Marta Kulis, Victor Segura, Anke Bergmann, et al. “Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.” Genome Res 25, no. 4 (April 2015): 478–87. https://doi.org/10.1101/gr.180240.114.
       Full Text  Link to Item
    • Jain, Swati, David C. Richardson, and Jane S. Richardson. “Computational Methods for RNA Structure Validation and Improvement.” Methods Enzymol 558 (2015): 181–212. https://doi.org/10.1016/bs.mie.2015.01.007.
       Full Text  Open Access Copy  Link to Item
    • Kapral, Gary J., Swati Jain, Jonas Noeske, Jennifer A. Doudna, David C. Richardson, and Jane S. Richardson. “New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.” Nucleic Acids Res 42, no. 20 (November 10, 2014): 12833–46. https://doi.org/10.1093/nar/gku992.
       Full Text  Open Access Copy  Link to Item
    • Deis, Lindsay N., Charles W. Pemble, Yang Qi, Andrew Hagarman, David C. Richardson, Jane S. Richardson, and Terrence G. Oas. “Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity.” Structure 22, no. 10 (October 7, 2014): 1467–77. https://doi.org/10.1016/j.str.2014.08.014.
       Full Text  Open Access Copy  Link to Item
    • Chen, Lu, Myrto Kostadima, Joost H. A. Martens, Giovanni Canu, Sara P. Garcia, Ernest Turro, Kate Downes, et al. “Transcriptional diversity during lineage commitment of human blood progenitors.” Science 345, no. 6204 (September 26, 2014): 1251033. https://doi.org/10.1126/science.1251033.
       Full Text  Link to Item
    • Richardson, Jane S., and David C. Richardson. “Biophysical highlights from 54 years of macromolecular crystallography.” Biophys J 106, no. 3 (February 4, 2014): 510–25. https://doi.org/10.1016/j.bpj.2014.01.001.
       Full Text  Link to Item
    • Richardson, Jane S., Michael G. Prisant, and David C. Richardson. “Crystallographic model validation: from diagnosis to healing.” Curr Opin Struct Biol 23, no. 5 (October 2013): 707–14. https://doi.org/10.1016/j.sbi.2013.06.004.
       Full Text  Link to Item
    • Richardson, Jane S., and David C. Richardson. “Studying and polishing the PDB's macromolecules.” Biopolymers 99, no. 3 (March 2013): 170–82. https://doi.org/10.1002/bip.22108.
       Full Text  Link to Item
    • Adams, Paul D., David Baker, Axel T. Brunger, Rhiju Das, Frank DiMaio, Randy J. Read, David C. Richardson, Jane S. Richardson, and Thomas C. Terwilliger. “Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.” Annu Rev Biophys 42 (2013): 265–87. https://doi.org/10.1146/annurev-biophys-083012-130253.
       Full Text  Link to Item
    • Richardson, J. S., and D. C. Richardson. “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, January 1, 2013, 1–10. https://doi.org/10.1007/978-94-007-6232-9_1.
       Full Text
    • Richardson, Jane S., and David C. Richardson. “Doing molecular biophysics: finding, naming, and picturing signal within complexity.” Annu Rev Biophys 42 (2013): 1–28. https://doi.org/10.1146/annurev-biophys-083012-130353.
       Full Text  Link to Item
    • Gainza, Pablo, Kyle E. Roberts, Ivelin Georgiev, Ryan H. Lilien, Daniel A. Keedy, Cheng-Yu Chen, Faisal Reza, et al. “OSPREY: protein design with ensembles, flexibility, and provable algorithms.” Methods Enzymol 523 (2013): 87–107. https://doi.org/10.1016/B978-0-12-394292-0.00005-9.
       Full Text  Link to Item
    • Echols, Nathaniel, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Jeffrey J. Headd, Airlie J. McCoy, et al. “Graphical tools for macromolecular crystallography in PHENIX.” Journal of Applied Crystallography 45, no. Pt 3 (June 2012): 581–86. https://doi.org/10.1107/s0021889812017293.
       Full Text
    • Headd, Jeffrey J., Nathaniel Echols, Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Vincent B. Chen, Nigel W. Moriarty, David C. Richardson, Jane S. Richardson, and Paul D. Adams. “Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.” Acta Crystallogr D Biol Crystallogr 68, no. Pt 4 (April 2012): 381–90. https://doi.org/10.1107/S0907444911047834.
       Full Text  Link to Item
    • Keedy, Daniel A., Ivelin Georgiev, Edward B. Triplett, Bruce R. Donald, David C. Richardson, and Jane S. Richardson. “The role of local backrub motions in evolved and designed mutations.” Plos Comput Biol 8, no. 8 (2012): e1002629. https://doi.org/10.1371/journal.pcbi.1002629.
       Full Text  Link to Item
    • Richardson, J. S., D. A. Keedy, and D. C. Richardson. ““The plot” thickens: More data, more dimensions, more uses,” January 1, 2012, 46–61. https://doi.org/10.1142/9789814449144_0004.
       Full Text
    • Adams, Paul D., Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Nathaniel Echols, Jeffrey J. Headd, Li-Wei Hung, et al. “The Phenix software for automated determination of macromolecular structures.” Methods 55, no. 1 (September 2011): 94–106. https://doi.org/10.1016/j.ymeth.2011.07.005.
       Full Text  Link to Item
    • Tyka, Michael D., Daniel A. Keedy, Ingemar André, Frank Dimaio, Yifan Song, David C. Richardson, Jane S. Richardson, and David Baker. “Alternate states of proteins revealed by detailed energy landscape mapping.” J Mol Biol 405, no. 2 (January 14, 2011): 607–18. https://doi.org/10.1016/j.jmb.2010.11.008.
       Full Text  Link to Item
    • Afonine, Pavel V., Ralf W. Grosse-Kunstleve, Vincent B. Chen, Jeffrey J. Headd, Nigel W. Moriarty, Jane S. Richardson, David C. Richardson, Alexandre Urzhumtsev, Peter H. Zwart, and Paul D. Adams. “phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.” Journal of Applied Crystallography 43, no. Pt 4 (August 2010): 669–76. https://doi.org/10.1107/s0021889810015608.
       Full Text
    • Adams, Paul D., Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Ian W. Davis, Nathaniel Echols, Jeffrey J. Headd, et al. “PHENIX: a comprehensive Python-based system for macromolecular structure solution.” Acta Crystallogr D Biol Crystallogr 66, no. Pt 2 (February 2010): 213–21. https://doi.org/10.1107/S0907444909052925.
       Full Text  Link to Item
    • Chen, Vincent B., W Bryan Arendall, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson, and David C. Richardson. “MolProbity: all-atom structure validation for macromolecular crystallography.” Acta Crystallogr D Biol Crystallogr 66, no. Pt 1 (January 2010): 12–21. https://doi.org/10.1107/S0907444909042073.
       Full Text  Link to Item
    • Morgan, Hugh, Tim Beck, Andrew Blake, Hilary Gates, Niels Adams, Guillaume Debouzy, Sophie Leblanc, et al. “EuroPhenome: a repository for high-throughput mouse phenotyping data.” Nucleic Acids Res 38, no. Database issue (January 2010): D577–85. https://doi.org/10.1093/nar/gkp1007.
       Full Text  Link to Item
    • Chen, Vincent B., Ian W. Davis, and David C. Richardson. “KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.” Protein Sci 18, no. 11 (November 2009): 2403–9. https://doi.org/10.1002/pro.250.
       Full Text  Link to Item
    • Adams, Paul D., Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Randy J. Read, Jane S. Richardson, David C. Richardson, and Thomas C. Terwilliger. “Recent developments in phasing and structure refinement for macromolecular crystallography.” Curr Opin Struct Biol 19, no. 5 (October 2009): 566–72. https://doi.org/10.1016/j.sbi.2009.07.014.
       Full Text  Link to Item
    • Headd, Jeffrey J., Robert M. Immormino, Daniel A. Keedy, Paul Emsley, David C. Richardson, and Jane S. Richardson. “Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.” J Struct Funct Genomics 10, no. 1 (March 2009): 83–93. https://doi.org/10.1007/s10969-008-9045-8.
       Full Text  Link to Item
    • Block, Jeremy N., David J. Zielinski, Vincent B. Chen, Ian W. Davis, E Claire Vinson, Rachael Brady, Jane S. Richardson, and David C. Richardson. “KinImmerse: Macromolecular VR for NMR ensembles.” Source Code Biol Med 4 (February 17, 2009): 3. https://doi.org/10.1186/1751-0473-4-3.
       Full Text  Link to Item
    • Keedy, Daniel A., Christopher J. Williams, Jeffrey J. Headd, W Bryan Arendall, Vincent B. Chen, Gary J. Kapral, Robert A. Gillespie, et al. “The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.” Proteins 77 Suppl 9, no. Suppl 9 (2009): 29–49. https://doi.org/10.1002/prot.22551.
       Full Text  Link to Item
    • Georgiev, Ivelin, Daniel Keedy, Jane S. Richardson, David C. Richardson, and Bruce R. Donald. “Algorithm for backrub motions in protein design.” Bioinformatics 24, no. 13 (July 1, 2008): i196–204. https://doi.org/10.1093/bioinformatics/btn169.
       Full Text  Link to Item
    • Richardson, Jane S., Bohdan Schneider, Laura W. Murray, Gary J. Kapral, Robert M. Immormino, Jeffrey J. Headd, David C. Richardson, et al. “RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).” Rna 14, no. 3 (March 2008): 465–81. https://doi.org/10.1261/rna.657708.
       Full Text  Link to Item
    • Wang, Xueyi, Gary Kapral, Laura Murray, David Richardson, Jane Richardson, and Jack Snoeyink. “RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.” J Math Biol 56, no. 1–2 (January 2008): 253–78. https://doi.org/10.1007/s00285-007-0082-x.
       Full Text  Link to Item
    • Tarpey, Patrick S., F Lucy Raymond, Lam S. Nguyen, Jayson Rodriguez, Anna Hackett, Lucianne Vandeleur, Raffaella Smith, et al. “Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.” Nature Genetics 39, no. 9 (September 2007): 1127–33. https://doi.org/10.1038/ng2100.
       Full Text
    • Field, Michael, Patrick S. Tarpey, Raffaella Smith, Sarah Edkins, Sarah O’Meara, Claire Stevens, Calli Tofts, et al. “Mutations in the BRWD3 gene cause X-linked mental retardation associated with macrocephaly.” Am J Hum Genet 81, no. 2 (August 2007): 367–74. https://doi.org/10.1086/520677.
       Full Text  Link to Item
    • Davis, Ian W., Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, et al. “MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.” Nucleic Acids Res 35, no. Web Server issue (July 2007): W375–83. https://doi.org/10.1093/nar/gkm216.
       Full Text  Link to Item
    • Kelley, Laura-Lee Clancy, Bret D. Dillard, Wolfram Tempel, Lirong Chen, Neil Shaw, Doowon Lee, M Gary Newton, et al. “Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution.” Acta Crystallogr Sect F Struct Biol Cryst Commun 63, no. Pt 7 (July 1, 2007): 549–52. https://doi.org/10.1107/S1744309107024049.
       Full Text  Link to Item
    • Greenman, Christopher, Philip Stephens, Raffaella Smith, Gillian L. Dalgliesh, Christopher Hunter, Graham Bignell, Helen Davies, et al. “Patterns of somatic mutation in human cancer genomes.” Nature 446, no. 7132 (March 8, 2007): 153–58. https://doi.org/10.1038/nature05610.
       Full Text  Link to Item
    • Gerwe, Brian, Laura-Lee Clancy Kelley, Bret D. Dillard, Thomas Lai, Zhi-Jie Liu, Wolfram Tempel, Lirong Chen, 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 8, no. 1 (March 2007): 1–10. https://doi.org/10.1007/s10969-007-9026-3.
       Full Text  Link to Item
    • Tarpey, Patrick S., F Lucy Raymond, Sarah O’Meara, Sarah Edkins, Jon Teague, Adam Butler, Ed Dicks, et al. “Mutations in CUL4B, which encodes a ubiquitin E3 ligase subunit, cause an X-linked mental retardation syndrome associated with aggressive outbursts, seizures, relative macrocephaly, central obesity, hypogonadism, pes cavus, and tremor.” Am J Hum Genet 80, no. 2 (February 2007): 345–52. https://doi.org/10.1086/511134.
       Full Text  Link to Item
    • Tarpey, Patrick S., Claire Stevens, Jon Teague, Sarah Edkins, Sarah O’Meara, Tim Avis, Syd Barthorpe, et al. “Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation.” Am J Hum Genet 79, no. 6 (December 2006): 1119–24. https://doi.org/10.1086/510137.
       Full Text  Link to Item
    • Ikediobi, Ogechi N., Helen Davies, Graham Bignell, Sarah Edkins, Claire Stevens, Sarah O’Meara, Thomas Santarius, et al. “Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.” Mol Cancer Ther 5, no. 11 (November 2006): 2606–12. https://doi.org/10.1158/1535-7163.MCT-06-0433.
       Full Text  Link to Item
    • Hunter, Chris, Raffaella Smith, Daniel P. Cahill, Philip Stephens, Claire Stevens, Jon Teague, Chris Greenman, et al. “A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy.” Cancer Res 66, no. 8 (April 15, 2006): 3987–91. https://doi.org/10.1158/0008-5472.CAN-06-0127.
       Full Text  Link to Item
    • Davis, Ian W., W Bryan Arendall, David C. Richardson, and Jane S. Richardson. “The backrub motion: how protein backbone shrugs when a sidechain dances.” Structure 14, no. 2 (February 2006): 265–74. https://doi.org/10.1016/j.str.2005.10.007.
       Full Text  Link to Item
    • Xu, Hao, Cheng Yang, Lirong Chen, Irina A. Kataeva, Wolfram Tempel, Doowon Lee, Jeff E. Habel, et al. “Away from the edge II: in-house Se-SAS phasing with chromium radiation.” Acta Crystallogr D Biol Crystallogr 61, no. Pt 7 (July 2005): 960–66. https://doi.org/10.1107/S0907444905010644.
       Full Text  Link to Item
    • Liu, Zhi-Jie, Wolfram Tempel, Joseph D. Ng, Dawei Lin, Ashit K. Shah, Lirong Chen, Peter S. Horanyi, et al. “The high-throughput protein-to-structure pipeline at SECSG.” Acta Crystallogr D Biol Crystallogr 61, no. Pt 6 (June 2005): 679–84. https://doi.org/10.1107/S0907444905013132.
       Full Text  Link to Item
    • Murray, L. J. W., J. S. Richardson, W. B. Arendall, and D. C. Richardson. “RNA backbone rotamers--finding your way in seven dimensions.” Biochem Soc Trans 33, no. Pt 3 (June 2005): 485–87. https://doi.org/10.1042/BST0330485.
       Full Text  Link to Item
    • Booth, D., R. C. Bateman, R. Sirochman, D. C. Richardson, J. S. Richardson, S. W. Weiner, M. Farwell, and C. Putnam-Evans. “Assessment of molecular construction in undergraduate biochemistry.” Journal of Chemical Education 82, no. 12 (January 1, 2005): 1854–58. https://doi.org/10.1021/ed082p1854.
       Full Text
    • Arendall, W Bryan, Wolfram Tempel, Jane S. Richardson, Weihong Zhou, Shuren Wang, Ian W. Davis, Zhi-Jie Liu, et al. “A test of enhancing model accuracy in high-throughput crystallography.” J Struct Funct Genomics 6, no. 1 (2005): 1–11. https://doi.org/10.1007/s10969-005-3138-4.
       Full Text  Link to Item
    • Tempel, Wolfram, Zhi-Jie Liu, Florian D. Schubot, Ashit Shah, Michael V. Weinberg, Francis E. Jenney, W Bryan Arendall, et al. “Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin.” Proteins 57, no. 4 (December 1, 2004): 878–82. https://doi.org/10.1002/prot.20280.
       Full Text  Link to Item
    • Davis, Ian W., Laura Weston Murray, Jane S. Richardson, and David C. Richardson. “MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.” Nucleic Acids Res 32, no. Web Server issue (July 1, 2004): W615–19. https://doi.org/10.1093/nar/gkh398.
       Full Text  Link to Item
    • Murray, Laura J. W., W Bryan Arendall, David C. Richardson, and Jane S. Richardson. “RNA backbone is rotameric.” Proc Natl Acad Sci U S A 100, no. 24 (November 25, 2003): 13904–9. https://doi.org/10.1073/pnas.1835769100.
       Full Text  Link to Item
    • Lovell, Simon C., Ian W. Davis, W Bryan Arendall, Paul I. W. de Bakker, J Michael Word, Michael G. Prisant, Jane S. Richardson, and David C. Richardson. “Structure validation by Calpha geometry: phi,psi and Cbeta deviation.” Proteins 50, no. 3 (February 15, 2003): 437–50. https://doi.org/10.1002/prot.10286.
       Full Text  Link to Item
    • Richardson, Jane S., W Arendall Bryan, and David C. Richardson. “New tools and data for improving structures, using all-atom contacts.” Methods Enzymol 374 (2003): 385–412. https://doi.org/10.1016/s0076-6879(03)74018-x.
       Full Text  Link to Item
    • Richardson, Jane S., and David C. Richardson. “Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.” Proc Natl Acad Sci U S A 99, no. 5 (March 5, 2002): 2754–59. https://doi.org/10.1073/pnas.052706099.
       Full Text  Link to Item
    • Bateman, R. C., D. Booth, R. Sirochman, J. Richardson, and D. Richardson. “Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry.” Journal of Chemical Education 79, no. 5 (January 1, 2002): 551. https://doi.org/10.1021/ed079p551.
       Full Text
    • Richardson, D. C., and J. S. Richardson. “Teaching molecular 3-D literacy.” Biochemistry and Molecular Biology Education 30, no. 1 (January 1, 2002): 21–26. https://doi.org/10.1002/bmb.2002.494030010005.
       Full Text
    • Word, J. M., R. C. Bateman, B. K. Presley, S. C. Lovell, and D. C. Richardson. “Exploring steric constraints on protein mutations using MAGE/PROBE.” Protein Sci 9, no. 11 (November 2000): 2251–59. https://doi.org/10.1110/ps.9.11.2251.
       Full Text  Link to Item
    • Lovell, S. C., J. M. Word, J. S. Richardson, and D. C. Richardson. “The penultimate rotamer library.” Proteins 40, no. 3 (August 15, 2000): 389–408.
       Link to Item
    • Grell, D., J. S. Richardson, D. C. Richardson, and M. Mutter. “SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics.” J Mol Graph Model 18, no. 3 (June 2000): 290–310. https://doi.org/10.1016/s1093-3263(00)00049-8.
       Full Text  Link to Item
    • Word, J. M., S. C. Lovell, J. S. Richardson, and D. C. Richardson. “Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.” J Mol Biol 285, no. 4 (January 29, 1999): 1735–47. https://doi.org/10.1006/jmbi.1998.2401.
       Full Text  Link to Item
    • Word, J. M., S. C. Lovell, T. H. LaBean, H. C. Taylor, M. E. Zalis, B. K. Presley, J. S. Richardson, and D. C. Richardson. “Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.” J Mol Biol 285, no. 4 (January 29, 1999): 1711–33. https://doi.org/10.1006/jmbi.1998.2400.
       Full Text  Link to Item
    • Lovell, S. C., J. M. Word, J. S. Richardson, and D. C. Richardson. “Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.” Proc Natl Acad Sci U S A 96, no. 2 (January 19, 1999): 400–405. https://doi.org/10.1073/pnas.96.2.400.
       Full Text  Link to Item
    • Gernert, K. M., B. D. Thomas, J. C. Plurad, J. S. Richardson, D. C. Richardson, and L. D. Bergman. “Puzzle pieces defined: locating common packing units in tertiary protein contacts.” Pac Symp Biocomput, 1996, 331–49.
       Link to Item
    • Varshney, A., F. P. Brooks, D. C. Richardson, W. V. Wright, and D. Manocha. “Defining, computing, and visualizing molecular interfaces.” Proceedings of the Ieee Visualization Conference, December 1, 1995, 36–43.
    • Gernert, K. M., M. C. Surles, T. H. Labean, J. S. Richardson, and D. C. Richardson. “The Alacoil: a very tight, antiparallel coiled-coil of helices.” Protein Sci 4, no. 11 (November 1995): 2252–60. https://doi.org/10.1002/pro.5560041102.
       Full Text  Link to Item
    • Bergman, L. D., J. S. Richardson, and D. C. Richardson. “An algorithm for smoothly tessellating beta-sheet structures in proteins.” J Mol Graph 13, no. 1 (February 1995): 36–58. https://doi.org/10.1016/0263-7855(94)00003-b.
       Full Text  Link to Item
    • Hemmingsen, J. M., K. M. Gernert, J. S. Richardson, and D. C. Richardson. “The tyrosine corner: a feature of most Greek key beta-barrel proteins.” Protein Sci 3, no. 11 (November 1994): 1927–37. https://doi.org/10.1002/pro.5560031104.
       Full Text  Link to Item
    • Quinn, T. P., N. B. Tweedy, R. W. Williams, J. S. Richardson, and D. C. Richardson. “Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein.” Proc Natl Acad Sci U S A 91, no. 19 (September 13, 1994): 8747–51. https://doi.org/10.1073/pnas.91.19.8747.
       Full Text  Link to Item
    • Richardson, D. C., and J. S. Richardson. “Kinemages--simple macromolecular graphics for interactive teaching and publication.” Trends Biochem Sci 19, no. 3 (March 1994): 135–38. https://doi.org/10.1016/0968-0004(94)90207-0.
       Full Text  Link to Item
    • Surles, M. C., J. S. Richardson, D. C. Richardson, and F. P. Brooks. “Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.” Protein Sci 3, no. 2 (February 1994): 198–210. https://doi.org/10.1002/pro.5560030205.
       Full Text  Link to Item
    • Bergman, L. D., J. S. Richardson, D. C. Richardson, and F. P. Brooks. “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, September 1, 1993, 117–26. https://doi.org/10.1145/166117.166132.
       Full Text
    • Gernert, R. M., J. S. Richardson, and D. C. Richardson. “Structural characteristics of felix, a designed protein.” Protein Engineering, Design and Selection 6 (January 1, 1993): 114. https://doi.org/10.1093/protein/6.Supplement.114-a.
       Full Text
    • Hemmingsen, J. M., J. S. Richardson, and D. C. Richardson. “A common arch structure in beta sandwich proteins: The tyrosine turn.” Protein Engineering, Design and Selection 6 (January 1, 1993): 104. https://doi.org/10.1093/protein/6.Supplement.104.
       Full Text
    • Richardson, J. S., D. C. Richardson, N. B. Tweedy, K. M. Gernert, T. P. Quinn, M. H. Hecht, B. W. Erickson, Y. Yan, R. D. McClain, and M. E. Donlan. “Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992.” Biophys J 63, no. 5 (November 1992): 1185–1209.
       Link to Item
    • Richardson, D. C., and J. S. Richardson. “The kinemage: a tool for scientific communication.” Protein Sci 1, no. 1 (January 1992): 3–9. https://doi.org/10.1002/pro.5560010102.
       Full Text  Link to Item
    • Hecht, M. H., J. S. Richardson, D. C. Richardson, and R. C. Ogden. “De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.” Science 249, no. 4971 (August 24, 1990): 884–91. https://doi.org/10.1126/science.2392678.
       Full Text  Link to Item
    • Harrison, R., and D. Richardson. “Bitewing radiographs of children taken with and without a film-holding device.” Dentomaxillofac Radiol 18, no. 3 (August 1989): 97–99. https://doi.org/10.1259/dmfr.18.3.2637884.
       Full Text  Link to Item
    • Richardson, J. S., and D. C. Richardson. “The de novo design of protein structures.” Trends Biochem Sci 14, no. 7 (July 1989): 304–9. https://doi.org/10.1016/0968-0004(89)90070-4.
       Full Text  Link to Item
    • Richardson, J. S., and D. C. Richardson. “Amino acid preferences for specific locations at the ends of alpha helices.” Science 240, no. 4859 (June 17, 1988): 1648–52. https://doi.org/10.1126/science.3381086.
       Full Text  Link to Item
    • Richardson, J. S., and D. C. Richardson. “Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal.” Proteins 4, no. 4 (1988): 229–39. https://doi.org/10.1002/prot.340040402.
       Full Text  Link to Item
    • Richardson, J., and D. Richardson. “Erratum: Amino acid preferences for specific locations at the ends of α helices (Science (1988) (1648)).” Science 242, no. 4886 (January 1, 1988): 1624. https://doi.org/10.1126/science.242.4886.1624-b.
       Full Text
    • McRee, D. E., D. C. Richardson, J. S. Richardson, and L. M. Siegel. “The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase.” J Biol Chem 261, no. 22 (August 5, 1986): 10277–81.
       Link to Item
    • McRee, D. E., D. C. Richardson, J. S. Richardson, and L. M. Siegel. “The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase.” Journal of Biological Chemistry 261, no. 22 (January 1, 1986): 10277–81.
    • McRee, D. E., J. S. Richardson, and D. C. Richardson. “Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli.” J Mol Biol 182, no. 3 (April 5, 1985): 467–68. https://doi.org/10.1016/0022-2836(85)90205-0.
       Full Text  Link to Item
    • Richardson, J. S., and D. C. Richardson. “Interpretation of electron density maps.” Methods Enzymol 115 (1985): 189–206. https://doi.org/10.1016/0076-6879(85)15016-0.
       Full Text  Link to Item
    • Unson, C. G., B. W. Erickson, D. C. Richardson, and J. S. Richardson. “Protein engineering: Design and synthesis of a protein.” Federation Proceedings 43, no. 6 (January 1, 1984).
    • Getzoff, E. D., J. A. Tainer, P. K. Weiner, P. A. Kollman, J. S. Richardson, and D. C. Richardson. “Electrostatic recognition between superoxide and copper, zinc superoxide dismutase.” Nature 306, no. 5940 (November 17, 1983): 287–90. https://doi.org/10.1038/306287a0.
       Full Text  Link to Item
    • Tainer, J. A., E. D. Getzoff, J. S. Richardson, and D. C. Richardson. “Structure and mechanism of copper, zinc superoxide dismutase.” Nature 306, no. 5940 (November 17, 1983): 284–87. https://doi.org/10.1038/306284a0.
       Full Text  Link to Item
    • Tainer, J. A., E. D. Getzoff, K. M. Beem, J. S. Richardson, and D. C. Richardson. “Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.” J Mol Biol 160, no. 2 (September 15, 1982): 181–217. https://doi.org/10.1016/0022-2836(82)90174-7.
       Full Text  Link to Item
    • McRee, D. E., and D. C. Richardson. “Preliminary X-ray diffraction studies on the hemoprotein subunit of Escherichia coli sulfite reductase.” J Mol Biol 154, no. 1 (January 5, 1982): 179–80. https://doi.org/10.1016/0022-2836(82)90426-0.
       Full Text  Link to Item
    • Taylor, H. C., D. C. Richardson, J. S. Richardson, A. Wlodawer, A. Komoriya, and I. M. Chaikes. “"Active" conformation of an inactive semi-synthetic ribonuclease-S.” J Mol Biol 149, no. 2 (June 25, 1981): 313–17. https://doi.org/10.1016/0022-2836(81)90305-3.
       Full Text  Link to Item
    • Richardson, J. S., J. A. Tainer, and D. C. Richardson. “An illustrated museum of protein structures.” Biophys J 32, no. 1 (October 1980): 211–13. https://doi.org/10.1016/S0006-3495(80)84934-4.
       Full Text  Link to Item
    • Richardson, J. S., E. D. Getzoff, and D. C. Richardson. “The beta bulge: a common small unit of nonrepetitive protein structure.” Proc Natl Acad Sci U S A 75, no. 6 (June 1978): 2574–78. https://doi.org/10.1073/pnas.75.6.2574.
       Full Text  Link to Item
    • Beem, K. M., D. C. Richardson, and K. V. Rajagopalan. “Metal sites of copper-zinc superoxide dismutase.” Biochemistry 16, no. 9 (May 3, 1977): 1930–36. https://doi.org/10.1021/bi00628a027.
       Full Text  Link to Item
    • Beem, K. M., J. S. Richardson, and D. C. Richardson. “Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies.” J Mol Biol 105, no. 2 (August 5, 1976): 327–32. https://doi.org/10.1016/0022-2836(76)90115-7.
       Full Text  Link to Item
    • Richardson, J. S., K. A. Thomas, and D. C. Richardson. “Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase.” Biochem Biophys Res Commun 63, no. 4 (April 21, 1975): 986–92. https://doi.org/10.1016/0006-291x(75)90666-x.
       Full Text  Link to Item
    • Richardson, J., K. A. Thomas, B. H. Rubin, and D. C. Richardson. “Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands.” Proc Natl Acad Sci U S A 72, no. 4 (April 1975): 1349–53. https://doi.org/10.1073/pnas.72.4.1349.
       Full Text  Link to Item
    • Thomas, K. A., B. H. Rubin, C. J. Bier, J. S. Richardson, and D. C. Richardson. “The crystal structure of bovine Cu2+,Zn2+ superoxide dismutase at 5.5-A resolution.” J Biol Chem 249, no. 17 (September 10, 1974): 5677–83.
       Link to Item
    • Richardson, D. C., C. J. Bier, and J. S. Richardson. “Two crystal forms of bovine superoxide dismutase.” J Biol Chem 247, no. 19 (October 10, 1972): 6368–69.
       Link to Item
    • Arnone, A., C. J. Bier, F. A. Cotton, V. W. Day, E. E. Hazen, D. C. Richardson, A. Yonath, and J. S. Richardson. “A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing.” J Biol Chem 246, no. 7 (April 10, 1971): 2302–16.
       Link to Item
    • Arnone, A., C. J. Bier, F. A. Cotton, E. E. Hazen, D. C. Richardson, and J. S. Richardson. “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 64, no. 2 (October 1969): 420–27. https://doi.org/10.1073/pnas.64.2.420.
       Full Text  Link to Item
    • Cotton, F. A., and D. C. Richardson. “Molecular Structure and Bonding in Diethylenetriaminechromium Tricarbonyl: The Cr(0) and Approximate Mn(0) Radii.” Inorganic Chemistry 5, no. 11 (November 1966): 1851–54. https://doi.org/10.1021/ic50045a003.
       Full Text
    • Cotton, F. A., E. E. Hazen, and D. C. Richardson. “Crystalline extracellular nuclease of Staphylococcus aureus.” J Biol Chem 241, no. 19 (October 10, 1966): 4389–90.
       Link to Item
    • Haight, G. P., David C. Richardson, and Nancy Hall Coburn. “A Spectrophotometric Study of Equilibria Involving Mononuclear Chromium(VI) Species in Solutions of Various Acids.” Inorganic Chemistry 3, no. 12 (December 1964): 1777–80. https://doi.org/10.1021/ic50022a028.
       Full Text

  • Conference Papers

    • Dicks, E., J. W. Teague, P. Stephens, K. Raine, A. Yates, C. Mattocks, P. Tarpey, et al. “AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.” In Bioinformatics, 23:1689–91, 2007. https://doi.org/10.1093/bioinformatics/btm152.
       Full Text  Link to Item
• Teaching & Mentoring
• 

  Recent Courses

  • BIOCHEM 393: Research Independent Study 2022
  • BIOCHEM 593: Research Independent Study 2022
  • BIOCHEM 393: Research Independent Study 2021
  • BIOCHEM 593: Research Independent Study 2021
  • BIOCHEM 622: Structure of Biological Macromolecules 2021
  • CBB 622: Structure of Biological Macromolecules 2021
  • SBB 622: Structure of Biological Macromolecules 2021

Some information on this profile has been compiled automatically from Duke databases and external sources. (Our About page explains how this works.) If you see a problem with the information, please write to Scholars@Duke and let us know. We will reply promptly.