David C. Richardson | Scholars@Duke

David C. Richardson
Professor of Biochemistry

Protein structure, folding, and design; 3D computer graphics; x-ray crystallography.

Current Appointments & Affiliations

Professor of Biochemistry, Biochemistry, Basic Science Departments 1991

Contact Information

132 Nanaline H Duke, Durham, NC 27710
Duke Box 3711, Durham, NC 27710
dcr@kinemage.biochem.duke.edu (919) 684-6010

Background
Education, Training, & Certifications
- Ph.D., Massachusetts Institute of Technology 1968
Duke Appointment History
- Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 1969 - 2019
Recognition
Awards & Honors
Expertise
Subject Headings
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
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- PHENIX: New methods for automation in macromolecular crystallography 2006 - 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 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 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 1993 - 1996
- Macromolecular Crystallography And Protein Chemistry 1990 - 1991
- Crystallographic Analysis Of Protein Structures awarded by National Institutes of Health 1987 - 1989
Publications & Artistic Works
Selected Publications
- Academic Articles
  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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, May 8, 2013, 1–10. https://doi.org/10.1007/978-94-007-6232-9-1.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.” J Appl Crystallogr 45, no. Pt 3 (June 1, 2012): 581–86. https://doi.org/10.1107/S0021889812017293.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.” J Appl Crystallogr 43, no. Pt 4 (August 1, 2010): 669–76. https://doi.org/10.1107/S0021889810015608.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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 (2009): 29–49. https://doi.org/10.1002/prot.22551.
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  - 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.
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  - 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.
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  - 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.
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  - 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.” Nat Genet 39, no. 9 (September 2007): 1127–33. https://doi.org/10.1038/ng2100.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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 (December 1, 2005): 1854–58.
  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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, January 1, 1993, 117–26. https://doi.org/10.1145/166117.166132.
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  - GERNERT, K. M., J. S. RICHARDSON, and D. C. RICHARDSON. “STRUCTURAL CHARACTERISTICS OF FELIX, A DESIGNED PROTEIN.” Protein Engineering 6 (1993): 114–114.
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  - HEMMINGSEN, J. M., J. S. RICHARDSON, and D. C. RICHARDSON. “A COMMON ARCH STRUCTURE IN BETA SANDWICH PROTEINS - THE TYROSINE TURN.” Protein Engineering 6 (1993): 104–104.
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  - 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.
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  - 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.
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  - 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.
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  - Harrison, R., and D. Richardson. “Bitewing radiographs of children taken with and without a film-holding device.” Dento Maxillo Facial Radiology 18, no. 3 (August 1989): 97–99. https://doi.org/10.1259/dmfr.18.3.2637884.
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  - 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.
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  - 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.
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  - 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.
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  - 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 (1988): 1624-.
  - 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.
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  - 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.
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  - 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.
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  - 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 (1984): no.-2457.
  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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- 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.
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