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
Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 1969

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
Recognition
Awards & Honors
Expertise
Subject Headings
Research
Selected Grants
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine awarded by National Institutes of Health 2015 - 2019
- Occurrence and Functional Roles of High Energy Base Pairs in DNA awarded by National Institutes of Health 2015 - 2019
- PHENIX: New methods for automation in macromolecular crystallography awarded by Ernest Orlando Lawrence Berkeley National Laboratory 2006 - 2019
- Structural Biology and Biophysics Training Program awarded by National Institutes of Health 1994 - 2015
- 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
- Molecular mechanisms of nitrosative stress resistance awarded by National Institutes of Health 1999 - 2005
- Analysis and Design of Protein Structures awarded by National Institutes of Health 1984 - 2004
- All-Atom Contact Analysis in Improving Structure Quality awarded by National Institutes of Health 2001 - 2004
- 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
  - Richardson, JS, Williams, CJ, Videau, LL, Chen, VB, and Richardson, DC. "Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale." Journal of Structural Biology 204, no. 2 (November 2018): 301-312. Full Text
  - Richardson, JS, Williams, CJ, Hintze, BJ, Chen, VB, Prisant, MG, Videau, LL, and Richardson, DC. "Model validation: local diagnosis, correction and when to quit." Acta Crystallographica. Section D, Structural Biology 74, no. Pt 2 (February 2018): 132-142. Full Text
  - Williams, CJ, Headd, JJ, Moriarty, NW, Prisant, MG, Videau, LL, Deis, LN, Verma, V, Keedy, DA, Hintze, BJ, Chen, VB, Jain, S, Lewis, SM, Arendall, WB, Snoeyink, J, Adams, PD, Lovell, SC, Richardson, JS, and Richardson, DC. "MolProbity: More and better reference data for improved all-atom structure validation." Protein Science : a Publication of the Protein Society 27, no. 1 (January 2018): 293-315. Full Text
  - Hintze, BJ, Richardson, JS, and Richardson, DC. "Mismodeled purines: implicit alternates and hidden Hoogsteens." Acta Crystallographica. Section D, Structural Biology 73, no. Pt 10 (October 2, 2017): 852-859. Full Text
  - Zheng-Bradley, X, Streeter, I, Fairley, S, Richardson, D, Clarke, L, Flicek, P, and 1000 Genomes Project Consortium, . "Alignment of 1000 Genomes Project reads to reference assembly GRCh38." Gigascience 6, no. 7 (July 2017): 1-8. Full Text
  - Richardson, JS, Videau, LL, Williams, CJ, and Richardson, DC. "Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding." Journal of molecular biology 429, no. 9 (May 2017): 1321-1335. Full Text
  - Ecker, S, Chen, L, Pancaldi, V, Bagger, FO, Fernández, JM, Carrillo de Santa Pau, E, Juan, D, Mann, AL, Watt, S, Casale, FP, Sidiropoulos, N, Rapin, N, Merkel, A, BLUEPRINT Consortium, , Stunnenberg, HG, Stegle, O, Frontini, M, Downes, K, Pastinen, T, Kuijpers, TW, Rico, D, Valencia, A, Beck, S, Soranzo, N, and Paul, DS. "Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types." Genome Biology 18, no. 1 (January 26, 2017): 18-null. Full Text
  - Chen, L, Ge, B, Casale, FP, Vasquez, L, Kwan, T, Garrido-Martín, D, Watt, S, Yan, Y, Kundu, K, Ecker, S, Datta, A, Richardson, D, Burden, F, Mead, D, Mann, AL, Fernandez, JM, Rowlston, S, Wilder, SP, Farrow, S, Shao, X, Lambourne, JJ, Redensek, A, Albers, CA, Amstislavskiy, V, Ashford, S, Berentsen, K, Bomba, L, Bourque, G, Bujold, D, Busche, S, Caron, M, Chen, S-H, Cheung, W, Delaneau, O, Dermitzakis, ET, Elding, H, Colgiu, I, Bagger, FO, Flicek, P, Habibi, E, Iotchkova, V, Janssen-Megens, E, Kim, B, Lehrach, H, Lowy, E, Mandoli, A, Matarese, F, Maurano, MT, Morris, JA, Pancaldi, V, Pourfarzad, F, Rehnstrom, K, Rendon, A, Risch, T, Sharifi, N, Simon, M-M, Sultan, M, Valencia, A, Walter, K, Wang, S-Y, Frontini, M, Antonarakis, SE, Clarke, L, Yaspo, M-L, Beck, S, Guigo, R, Rico, D, Martens, JHA, Ouwehand, WH, Kuijpers, TW, Paul, DS, Stunnenberg, HG, Stegle, O, Downes, K, Pastinen, T, and Soranzo, N. "Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells." Cell 167, no. 5 (November 2016): 1398-1414.e24. Full Text
  - Fernández, JM, de la Torre, V, Richardson, D, Royo, R, Puiggròs, M, Moncunill, V, Fragkogianni, S, Clarke, L, Flicek, P, Rico, D, Torrents, D, Carrillo de Santa Pau, E, and Valencia, A. "The BLUEPRINT Data Analysis Portal." Cell Systems 3, no. 5 (November 2016): 491-495.e5. Full Text
  - Javierre, BM, Burren, OS, Wilder, SP, Kreuzhuber, R, Hill, SM, Sewitz, S, Cairns, J, Wingett, SW, Várnai, C, Thiecke, MJ, Burden, F, Farrow, S, Cutler, AJ, Rehnström, K, Downes, K, Grassi, L, Kostadima, M, Freire-Pritchett, P, Wang, F, BLUEPRINT Consortium, , Stunnenberg, HG, Todd, JA, Zerbino, DR, Stegle, O, Ouwehand, WH, Frontini, M, Wallace, C, Spivakov, M, and Fraser, P. "Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters." Cell 167, no. 5 (November 2016): 1369-1384.e19. Full Text
  - Stunnenberg, HG, International Human Epigenome Consortium, , and Hirst, M. "The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery." Cell 167, no. 5 (November 2016): 1145-1149. Full Text
  - Hintze, BJ, Lewis, SM, Richardson, JS, and Richardson, DC. "Molprobity's ultimate rotamer-library distributions for model validation." Proteins 84, no. 9 (September 2016): 1177-1189. Full Text
  - Hintze, BJ, Lewis, SM, Richardson, JS, and Richardson, DC. "Cover Image, Volume 84, Issue 9." Proteins: Structure, Function, and Bioinformatics 84, no. 9 (September 2016): C1-C1. Full Text
  - Kulis, M, Merkel, A, Heath, S, Queirós, AC, Schuyler, RP, Castellano, G, Beekman, R, Raineri, E, Esteve, A, Clot, G, Verdaguer-Dot, N, Duran-Ferrer, M, Russiñol, N, Vilarrasa-Blasi, R, Ecker, S, Pancaldi, V, Rico, D, Agueda, L, Blanc, J, Richardson, D, Clarke, L, Datta, A, Pascual, M, Agirre, X, Prosper, F, Alignani, D, Paiva, B, Caron, G, Fest, T, Muench, MO, Fomin, ME, Lee, S-T, Wiemels, JL, Valencia, A, Gut, M, Flicek, P, Stunnenberg, HG, Siebert, R, Küppers, R, Gut, IG, Campo, E, and Martín-Subero, JI. "Whole-genome fingerprint of the DNA methylome during human B cell differentiation." Nature Genetics 47, no. 7 (July 2015): 746-756. Full Text
  - Agirre, X, Castellano, G, Pascual, M, Heath, S, Kulis, M, Segura, V, Bergmann, A, Esteve, A, Merkel, A, Raineri, E, Agueda, L, Blanc, J, Richardson, D, Clarke, L, Datta, A, Russiñol, N, Queirós, AC, Beekman, R, Rodríguez-Madoz, JR, San José-Enériz, E, Fang, F, Gutiérrez, NC, García-Verdugo, JM, Robson, MI, Schirmer, EC, Guruceaga, E, Martens, JHA, Gut, M, Calasanz, MJ, Flicek, P, Siebert, R, Campo, E, Miguel, JFS, Melnick, A, Stunnenberg, HG, Gut, IG, Prosper, F, and Martín-Subero, JI. "Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers." Genome Research 25, no. 4 (April 2015): 478-487. Full Text
  - Jain, S, Richardson, DC, and Richardson, JS. "Computational Methods for RNA Structure Validation and Improvement." Methods in Enzymology 558 (January 2015): 181-212. Full Text Open Access Copy
  - Jain, S, Richardson, DC, and Richardson, JS. "Computational Methods for RNA Structure Validation and Improvement." Methods in Enzymology (2015). Full Text
  - Kapral, GJ, Jain, S, Noeske, J, Doudna, JA, Richardson, DC, and Richardson, JS. "New tools provide a second look at HDV ribozyme structure, dynamics and cleavage." Nucleic acids research 42, no. 20 (November 2014): 12833-12846. Full Text Open Access Copy
  - Deis, LN, Pemble, CW, Qi, Y, Hagarman, A, Richardson, DC, Richardson, JS, and Oas, TG. "Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity." Structure (London, England : 1993) 22, no. 10 (October 2014): 1467-1477. Full Text Open Access Copy
  - Chen, L, Kostadima, M, Martens, JHA, Canu, G, Garcia, SP, Turro, E, Downes, K, Macaulay, IC, Bielczyk-Maczynska, E, Coe, S, Farrow, S, Poudel, P, Burden, F, Jansen, SBG, Astle, WJ, Attwood, A, Bariana, T, de Bono, B, Breschi, A, Chambers, JC, Consortium, B, Choudry, FA, Clarke, L, Coupland, P, van der Ent, M, Erber, WN, Jansen, JH, Favier, R, Fenech, ME, Foad, N, Freson, K, van Geet, C, Gomez, K, Guigo, R, Hampshire, D, Kelly, AM, Kerstens, HHD, Kooner, JS, Laffan, M, Lentaigne, C, Labalette, C, Martin, T, Meacham, S, Mumford, A, Nürnberg, S, Palumbo, E, van der Reijden, BA, Richardson, D, Sammut, SJ, Slodkowicz, G, Tamuri, AU, Vasquez, L, Voss, K, Watt, S, Westbury, S, Flicek, P, Loos, R, Goldman, N, Bertone, P, Read, RJ, Richardson, S, Cvejic, A, Soranzo, N, Ouwehand, WH, Stunnenberg, HG, Frontini, M, and Rendon, A. "Transcriptional diversity during lineage commitment of human blood progenitors." Science (New York, N.Y.) 345, no. 6204 (September 2014): 1251033-null. Full Text
  - Richardson, JS, and Richardson, DC. "Biophysical highlights from 54 years of macromolecular crystallography." Biophysical journal 106, no. 3 (February 2014): 510-525. (Review) Full Text
  - Capp, JA, Hagarman, A, Richardson, DC, and Oas, TG. "The statistical conformation of a highly flexible protein: Small-angle x-ray scattering of S. aureus protein A." Structure 22, no. 8 (2014): 1184-1195. Full Text
  - Richardson, JS, Prisant, MG, and Richardson, DC. "Crystallographic model validation: from diagnosis to healing." Curr Opin Struct Biol 23, no. 5 (October 2013): 707-714. (Review) Full Text Link to Item
  - Richardson, JS, and Richardson, DC. "Studying and polishing the PDB's macromolecules." Biopolymers 99, no. 3 (March 2013): 170-182. (Review) Full Text Link to Item
  - Richardson, JS, and Richardson, DC. "Invited review: Studying and polishing the PDB's macromolecules." Biopolymers 99, no. 3 (March 1, 2013): 170-182. (Review) Full Text
  - Adams, PD, Baker, D, Brunger, AT, Das, R, DiMaio, F, Read, RJ, Richardson, DC, Richardson, JS, and Terwilliger, TC. "Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems." Annual Review of Biophysics 42 (January 2013): 265-287. (Review) Full Text
  - Gainza, P, Roberts, KE, Georgiev, I, Lilien, RH, Keedy, DA, Chen, C-Y, Reza, F, Anderson, AC, Richardson, DC, Richardson, JS, and Donald, BR. "OSPREY: protein design with ensembles, flexibility, and provable algorithms." Methods in Enzymology 523 (January 2013): 87-107. Full Text
  - Richardson, JS, Prisant, MG, and Richardson, DC. "Crystallographic model validation: From diagnosis to healing." Current Opinion in Structural Biology 23, no. 5 (2013): 707-714. Full Text
  - Richardson, JS, and Richardson, DC. "Doing molecular biophysics: finding, naming, and picturing signal within complexity." Annu Rev Biophys 42 (2013): 1-28. Full Text Link to Item
  - Richardson, JS, and Richardson, DC. "The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest!." NATO Science for Peace and Security Series A: Chemistry and Biology (2013): 1-10. Full Text
  - Echols, N, Grosse-Kunstleve, RW, Afonine, PV, Bunkóczi, G, Chen, VB, Headd, JJ, McCoy, AJ, Moriarty, NW, Read, RJ, Richardson, DC, Richardson, JS, Terwilliger, TC, and Adams, PD. "Graphical tools for macromolecular crystallography in PHENIX." Journal of Applied Crystallography 45, no. Pt 3 (June 2012): 581-586. Full Text
  - Headd, JJ, Echols, N, Afonine, PV, Grosse-Kunstleve, RW, Chen, VB, Moriarty, NW, Richardson, DC, Richardson, JS, and Adams, PD. "Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution." Acta Crystallographica. Section D, Biological Crystallography 68, no. Pt 4 (April 2012): 381-390. Full Text
  - Keedy, DA, Georgiev, I, Triplett, EB, Donald, BR, Richardson, DC, and Richardson, JS. "The role of local backrub motions in evolved and designed mutations." Plos Computational Biology 8, no. 8 (January 2012): e1002629-null. Full Text
  - Richardson, JS, Keedy, DA, and Richardson, DC. "“The plot” thickens: More data, more dimensions, more uses." (January 1, 2012): 46-61. (Chapter) Full Text
  - Adams, PD, Afonine, PV, Bunkóczi, G, Chen, VB, Echols, N, Headd, JJ, Hung, L-W, Jain, S, Kapral, GJ, Grosse Kunstleve, RW, McCoy, AJ, Moriarty, NW, Oeffner, RD, Read, RJ, Richardson, DC, Richardson, JS, Terwilliger, TC, and Zwart, PH. "The Phenix software for automated determination of macromolecular structures." Methods (San Diego, Calif.) 55, no. 1 (September 2011): 94-106. Full Text
  - Tyka, MD, Keedy, DA, André, I, Dimaio, F, Song, Y, Richardson, DC, Richardson, JS, and Baker, D. "Alternate states of proteins revealed by detailed energy landscape mapping." Journal of Molecular Biology 405, no. 2 (January 2011): 607-618. Full Text
  - Afonine, PV, Grosse-Kunstleve, RW, Chen, VB, Headd, JJ, Moriarty, NW, Richardson, JS, Richardson, DC, Urzhumtsev, A, Zwart, PH, and Adams, PD. "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): 669-676. Full Text
  - Adams, PD, Afonine, PV, Bunkóczi, G, Chen, VB, Davis, IW, Echols, N, Headd, JJ, Hung, L-W, Kapral, GJ, Grosse-Kunstleve, RW, McCoy, AJ, Moriarty, NW, Oeffner, R, Read, RJ, Richardson, DC, Richardson, JS, Terwilliger, TC, and Zwart, PH. "PHENIX: a comprehensive Python-based system for macromolecular structure solution." Acta Crystallographica. Section D, Biological Crystallography 66, no. Pt 2 (February 2010): 213-221. Full Text
  - Chen, VB, Arendall, WB, Headd, JJ, Keedy, DA, Immormino, RM, Kapral, GJ, Murray, LW, Richardson, JS, and Richardson, DC. "MolProbity: all-atom structure validation for macromolecular crystallography." Acta Crystallographica. Section D, Biological Crystallography 66, no. Pt 1 (January 2010): 12-21. Full Text
  - Morgan, H, Beck, T, Blake, A, Gates, H, Adams, N, Debouzy, G, Leblanc, S, Lengger, C, Maier, H, Melvin, D, Meziane, H, Richardson, D, Wells, S, White, J, Wood, J, EUMODIC Consortium, , de Angelis, MH, Brown, SDM, Hancock, JM, and Mallon, A-M. "EuroPhenome: a repository for high-throughput mouse phenotyping data." Nucleic Acids Research 38, no. Database issue (January 2010): D577-D585. Full Text
  - Chen, VB, Davis, IW, and Richardson, DC. "KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program." Protein Science : a Publication of the Protein Society 18, no. 11 (November 2009): 2403-2409. Full Text
  - Headd, JJ, Immormino, RM, Keedy, DA, Emsley, P, Richardson, DC, and Richardson, JS. "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. Full Text Link to Item
  - Block, JN, Zielinski, DJ, Chen, VB, Davis, IW, Vinson, EC, Brady, R, Richardson, JS, and Richardson, DC. "KinImmerse: Macromolecular VR for NMR ensembles." Source code for biology and medicine 4 (February 17, 2009): 3-. Full Text
  - Adams, PD, Afonine, PV, Grosse-Kunstleve, RW, Read, RJ, Richardson, JS, Richardson, DC, and Terwilliger, TC. "Recent developments in phasing and structure refinement for macromolecular crystallography." Current Opinion in Structural Biology 19, no. 5 (2009): 566-572. Full Text
  - Keedy, DA, Williams, CJ, Headd, JJ, Arendall, WB, Chen, VB, Kapral, GJ, Gillespie, RA, Block, JN, Zemla, A, Richardson, DC, and Richardson, JS. "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. Full Text Link to Item
  - Georgiev, I, Keedy, D, Richardson, JS, Richardson, DC, and Donald, BR. "Algorithm for backrub motions in protein design." Bioinformatics (Oxford, England) 24, no. 13 (July 2008): i196-i204. Full Text
  - Richardson, JS, Schneider, B, Murray, LW, Kapral, GJ, Immormino, RM, Headd, JJ, Richardson, DC, Ham, D, Hershkovits, E, Williams, LD, Keating, KS, Pyle, AM, Micallef, D, Westbrook, J, Berman, HM, and RNA Ontology Consortium, . "RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." Rna (New York, N.Y.) 14, no. 3 (March 2008): 465-481. Full Text
  - Wang, X, Kapral, G, Murray, L, Richardson, D, Richardson, J, and Snoeyink, J. "RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone." Journal of Mathematical Biology 56, no. 1-2 (January 2008): 253-278. Full Text
  - Tarpey, PS, Raymond, FL, Nguyen, LS, Rodriguez, J, Hackett, A, Vandeleur, L, Smith, R, Shoubridge, C, Edkins, S, Stevens, C, O'Meara, S, Tofts, C, Barthorpe, S, Buck, G, Cole, J, Halliday, K, Hills, K, Jones, D, Mironenko, T, Perry, J, Varian, J, West, S, Widaa, S, Teague, J, Dicks, E, Butler, A, Menzies, A, Richardson, D, Jenkinson, A, Shepherd, R, Raine, K, Moon, J, Luo, Y, Parnau, J, Bhat, SS, Gardner, A, Corbett, M, Brooks, D, Thomas, P, Parkinson-Lawrence, E, Porteous, ME, Warner, JP, Sanderson, T, Pearson, P, Simensen, RJ, Skinner, C, Hoganson, G, Superneau, D, Wooster, R, Bobrow, M, Turner, G, Stevenson, RE, Schwartz, CE, Futreal, PA, Srivastava, AK, Stratton, MR, and Gécz, J. "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): 1127-1133. Full Text
  - Field, M, Tarpey, PS, Smith, R, Edkins, S, O'Meara, S, Stevens, C, Tofts, C, Teague, J, Butler, A, Dicks, E, Barthorpe, S, Buck, G, Cole, J, Gray, K, Halliday, K, Hills, K, Jenkinson, A, Jones, D, Menzies, A, Mironenko, T, Perry, J, Raine, K, Richardson, D, Shepherd, R, Small, A, Varian, J, West, S, Widaa, S, Mallya, U, Wooster, R, Moon, J, Luo, Y, Hughes, H, Shaw, M, Friend, KL, Corbett, M, Turner, G, Partington, M, Mulley, J, Bobrow, M, Schwartz, C, Stevenson, R, Gecz, J, Stratton, MR, Futreal, PA, and Raymond, FL. "Mutations in the BRWD3 gene cause X-linked mental retardation associated with macrocephaly." American Journal of Human Genetics 81, no. 2 (August 2007): 367-374. Full Text
  - Davis, IW, Leaver-Fay, A, Chen, VB, Block, JN, Kapral, GJ, Wang, X, Murray, LW, Arendall, WB, Snoeyink, J, Richardson, JS, and Richardson, DC. "MolProbity: all-atom contacts and structure validation for proteins and nucleic acids." Nucleic Acids Research 35, no. Web Server issue (July 2007): W375-W383. Full Text
  - Kelley, L-LC, Dillard, BD, Tempel, W, Chen, L, Shaw, N, Lee, D, Newton, MG, Sugar, FJ, Jenney, FE, Lee, HS, Shah, C, Poole, FL, Adams, MWW, Richardson, JS, Richardson, DC, Liu, Z-J, Wang, B-C, and Rose, J. "Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution." Acta Crystallographica. Section F, Structural Biology and Crystallization Communications 63, no. Pt 7 (July 2007): 549-552. Full Text
  - Greenman, C, Stephens, P, Smith, R, Dalgliesh, GL, Hunter, C, Bignell, G, Davies, H, Teague, J, Butler, A, Stevens, C, Edkins, S, O'Meara, S, Vastrik, I, Schmidt, EE, Avis, T, Barthorpe, S, Bhamra, G, Buck, G, Choudhury, B, Clements, J, Cole, J, Dicks, E, Forbes, S, Gray, K, Halliday, K, Harrison, R, Hills, K, Hinton, J, Jenkinson, A, Jones, D, Menzies, A, Mironenko, T, Perry, J, Raine, K, Richardson, D, Shepherd, R, Small, A, Tofts, C, Varian, J, Webb, T, West, S, Widaa, S, Yates, A, Cahill, DP, Louis, DN, Goldstraw, P, Nicholson, AG, Brasseur, F, Looijenga, L, Weber, BL, Chiew, Y-E, DeFazio, A, Greaves, MF, Green, AR, Campbell, P, Birney, E, Easton, DF, Chenevix-Trench, G, Tan, M-H, Khoo, SK, Teh, BT, Yuen, ST, Leung, SY, Wooster, R, Futreal, PA, and Stratton, MR. "Patterns of somatic mutation in human cancer genomes." Nature 446, no. 7132 (March 2007): 153-158. Full Text
  - Tarpey, PS, Raymond, FL, O'Meara, S, Edkins, S, Teague, J, Butler, A, Dicks, E, Stevens, C, Tofts, C, Avis, T, Barthorpe, S, Buck, G, Cole, J, Gray, K, Halliday, K, Harrison, R, Hills, K, Jenkinson, A, Jones, D, Menzies, A, Mironenko, T, Perry, J, Raine, K, Richardson, D, Shepherd, R, Small, A, Varian, J, West, S, Widaa, S, Mallya, U, Moon, J, Luo, Y, Holder, S, Smithson, SF, Hurst, JA, Clayton-Smith, J, Kerr, B, Boyle, J, Shaw, M, Vandeleur, L, Rodriguez, J, Slaugh, R, Easton, DF, Wooster, R, Bobrow, M, Srivastava, AK, Stevenson, RE, Schwartz, CE, Turner, G, Gecz, J, Futreal, PA, Stratton, MR, and Partington, M. "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." American Journal of Human Genetics 80, no. 2 (February 2007): 345-352. Full Text
  - Gerwe, B, Kelley, L-LC, Dillard, BD, Lai, T, Liu, Z-J, Tempel, W, Chen, L, Habel, J, Lee, D, Jr, FEJ, Sugar, FJ, Richardson, JS, Richardson, DC, Newton, MG, Wang, B-C, Adams, MWW, and Rose, JP. "Structural and transcriptional analyses of a purine nucleotide-binding protein from Pyrococcus furiosus: A component of a novel, membrane-bound multiprotein complex unique to this hyperthermophilic archaeon." Journal of Structural and Functional Genomics 8, no. 1 (2007): 1-10. Full Text
  - Tarpey, PS, Stevens, C, Teague, J, Edkins, S, O'Meara, S, Avis, T, Barthorpe, S, Buck, G, Butler, A, Cole, J, Dicks, E, Gray, K, Halliday, K, Harrison, R, Hills, K, Hinton, J, Jones, D, Menzies, A, Mironenko, T, Perry, J, Raine, K, Richardson, D, Shepherd, R, Small, A, Tofts, C, Varian, J, West, S, Widaa, S, Yates, A, Catford, R, Butler, J, Mallya, U, Moon, J, Luo, Y, Dorkins, H, Thompson, D, Easton, DF, Wooster, R, Bobrow, M, Carpenter, N, Simensen, RJ, Schwartz, CE, Stevenson, RE, Turner, G, Partington, M, Gecz, J, Stratton, MR, Futreal, PA, and Raymond, FL. "Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation." American Journal of Human Genetics 79, no. 6 (December 2006): 1119-1124. Full Text
  - Ikediobi, ON, Davies, H, Bignell, G, Edkins, S, Stevens, C, O'Meara, S, Santarius, T, Avis, T, Barthorpe, S, Brackenbury, L, Buck, G, Butler, A, Clements, J, Cole, J, Dicks, E, Forbes, S, Gray, K, Halliday, K, Harrison, R, Hills, K, Hinton, J, Hunter, C, Jenkinson, A, Jones, D, Kosmidou, V, Lugg, R, Menzies, A, Mironenko, T, Parker, A, Perry, J, Raine, K, Richardson, D, Shepherd, R, Small, A, Smith, R, Solomon, H, Stephens, P, Teague, J, Tofts, C, Varian, J, Webb, T, West, S, Widaa, S, Yates, A, Reinhold, W, Weinstein, JN, Stratton, MR, Futreal, PA, and Wooster, R. "Mutation analysis of 24 known cancer genes in the NCI-60 cell line set." Molecular Cancer Therapeutics 5, no. 11 (November 6, 2006): 2606-2612. Full Text
  - Hunter, C, Smith, R, Cahill, DP, Stephens, P, Stevens, C, Teague, J, Greenman, C, Edkins, S, Bignell, G, Davies, H, O'Meara, S, Parker, A, Avis, T, Barthorpe, S, Brackenbury, L, Buck, G, Butler, A, Clements, J, Cole, J, Dicks, E, Forbes, S, Gorton, M, Gray, K, Halliday, K, Harrison, R, Hills, K, Hinton, J, Jenkinson, A, Jones, D, Kosmidou, V, Laman, R, Lugg, R, Menzies, A, Perry, J, Petty, R, Raine, K, Richardson, D, Shepherd, R, Small, A, Solomon, H, Tofts, C, Varian, J, West, S, Widaa, S, Yates, A, Easton, DF, Riggins, G, Roy, JE, Levine, KK, Mueller, W, Batchelor, TT, Louis, DN, Stratton, MR, Futreal, PA, and Wooster, R. "A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy." Cancer Research 66, no. 8 (April 2006): 3987-3991. Full Text
  - Davis, IW, Arendall, WB, Richardson, DC, and Richardson, JS. "The backrub motion: how protein backbone shrugs when a sidechain dances." Structure (London, England : 1993) 14, no. 2 (February 2006): 265-274. Full Text
  - Xu, H, Yang, C, Chen, L, Kataeva, IA, Tempel, W, Lee, D, Habel, JE, Nguyen, D, Pflugrath, JW, Ferrara, JD, Arendall, WB, Richardson, JS, Richardson, DC, Liu, ZJ, Newton, MG, Rose, JP, and Wang, BC. "Away from the edge II: in-house Se-SAS phasing with chromium radiation." Acta Crystallographica Section D: Biological Crystallography 61, no. Pt 7 (July 2005): 960-966. Full Text
  - Liu, Z-J, Tempel, W, Ng, JD, Lin, D, Shah, AK, Chen, L, Horanyi, PS, Habel, JE, Kataeva, IA, Xu, H, Yang, H, Chang, JC, Huang, L, Chang, S-H, Zhou, W, Lee, D, Praissman, JL, Zhang, H, Newton, MG, Rose, JP, Richardson, JS, Richardson, DC, and Wang, B-C. "The high-throughput protein-to-structure pipeline at SECSG." Acta Crystallographica Section D: Biological Crystallography 61, no. Pt 6 (June 2005): 679-684. Full Text
  - Murray, LJW, Richardson, JS, Arendall, WB, and Richardson, DC. "RNA backbone rotamers--finding your way in seven dimensions." Biochem Soc Trans 33, no. Pt 3 (June 2005): 485-487. Full Text Link to Item
  - Arendall, WB, Tempel, W, Richardson, JS, Zhou, W, Wang, S, Davis, IW, Liu, Z-J, Rose, JP, Carson, WM, Luo, M, Richardson, DC, and Wang, B-C. "A test of enhancing model accuracy in high-throughput crystallography." Journal of Structural and Functional Genomics 6, no. 1 (January 2005): 1-11. Full Text
  - Booth, D, Jr, RCB, Sirochman, R, Richardson, DC, Richardson, JS, Weiner, SW, Farwell, M, and Putnam-Evans, C. "Assessment of molecular construction in undergraduate biochemistry." Journal of Chemical Education 82, no. 12 (2005): 1854-1858.
  - Tempel, W, Liu, Z-J, Schubot, FD, Shah, A, Weinberg, MV, Jenney, FE, Arendall, WB, Adams, MWW, Richardson, JS, Richardson, DC, Rose, JP, and Wang, B-C. "Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin." Proteins 57, no. 4 (December 2004): 878-882. Full Text
  - Davis, IW, Murray, LW, Richardson, JS, and Richardson, DC. "MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes." Nucleic Acids Research 32, no. Web Server issue (July 2004): W615-W619. Full Text
  - Murray, LJW, Arendall, WB, Richardson, DC, and Richardson, JS. "RNA backbone is rotameric." Proceedings of the National Academy of Sciences of the United States of America 100, no. 24 (November 11, 2003): 13904-13909. Full Text
  - Lovell, SC, Davis, IW, Arendall, WB, de Bakker, PIW, Word, JM, Prisant, MG, Richardson, JS, and Richardson, DC. "Structure validation by Calpha geometry: phi,psi and Cbeta deviation." Proteins 50, no. 3 (February 2003): 437-450. Full Text
  - Richardson, JS, Bryan, WA, and Richardson, DC. "New tools and data for improving structures, using all-atom contacts." Methods in Enzymology 374 (January 2003): 385-412. Full Text
  - Richardson, JS, and Richardson, DC. "Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation." Proceedings of the National Academy of Sciences of the United States of America 99, no. 5 (March 2002): 2754-2759. Full Text
  - Jr, RCB, Booth, D, Sirochman, R, Richardson, J, and Richardson, D. "Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry." Journal of Chemical Education 79, no. 5 (2002): 551--.
  - Richardson, DC, and Richardson, JS. "Teaching molecular 3-D literacy." Biochemistry and Molecular Biology Education 30, no. 1 (2002): 21-26. Full Text
  - Word, JM, Bateman, RC, Presley, BK, Lovell, SC, and Richardson, DC. "Exploring steric constraints on protein mutations using MAGE/PROBE." Protein Sci 9, no. 11 (November 2000): 2251-2259. Full Text Link to Item
  - Lovell, SC, Word, JM, Richardson, JS, and Richardson, DC. "The penultimate rotamer library." Proteins 40, no. 3 (August 2000): 389-408. Full Text
  - Grell, D, Richardson, JS, Richardson, DC, and Mutter, M. "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. Link to Item
  - Lovell, SC, Word, JM, Richardson, JS, and Richardson, DC. "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. Link to Item
  - Word, JM, Lovell, SC, LaBean, TH, Taylor, HC, Zalis, ME, Presley, BK, Richardson, JS, and Richardson, DC. "Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms." Journal of Molecular Biology 285, no. 4 (January 1999): 1711-1733. Full Text
  - Word, JM, Lovell, SC, Richardson, JS, and Richardson, DC. "Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation." Journal of Molecular Biology 285, no. 4 (January 1999): 1735-1747. Full Text
  - Gernert, KM, Thomas, BD, Plurad, JC, Richardson, JS, Richardson, DC, and Bergman, LD. "Puzzle pieces defined: locating common packing units in tertiary protein contacts." Pac Symp Biocomput (1996): 331-349. Link to Item
  - Gernert, KM, Surles, MC, Labean, TH, Richardson, JS, and Richardson, DC. "The Alacoil: a very tight, antiparallel coiled-coil of helices." Protein Science : a Publication of the Protein Society 4, no. 11 (November 1995): 2252-2260. Full Text
  - Bergman, LD, Richardson, JS, and Richardson, DC. "An algorithm for smoothly tessellating beta-sheet structures in proteins." J Mol Graph 13, no. 1 (February 1995): 36-58. Link to Item
  - Varshney, A, Jr, FPB, Richardson, DC, Wright, WV, and Manocha, D. "Defining, computing, and visualizing molecular interfaces." Proceedings of the IEEE Visualization Conference (1995): 36-43.
  - Hemmingsen, JM, Gernert, KM, Richardson, JS, and Richardson, DC. "The tyrosine corner: a feature of most Greek key beta-barrel proteins." Protein Science : a Publication of the Protein Society 3, no. 11 (November 1994): 1927-1937. Full Text
  - Quinn, TP, Tweedy, NB, Williams, RW, Richardson, JS, and Richardson, DC. "Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein." Proceedings of the National Academy of Sciences of the United States of America 91, no. 19 (September 1994): 8747-8751. Full Text
  - Richardson, DC, and Richardson, JS. "Kinemages--simple macromolecular graphics for interactive teaching and publication." Trends Biochem Sci 19, no. 3 (March 1994): 135-138. Link to Item
  - Surles, MC, Richardson, JS, Richardson, DC, and Brooks, FP. "Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system." Protein Sci 3, no. 2 (February 1994): 198-210. (Review) Full Text Link to Item
  - Bergman, LD, and Richardson, JS. "VIEW-An exploratory molecular visualization system with user-definable interaction sequences." Proc ACM SIGGRAPH 93 Conf Comput Graphics (1993): 117-126.
  - GERNERT, KM, RICHARDSON, JS, and RICHARDSON, DC. "STRUCTURAL CHARACTERISTICS OF FELIX, A DESIGNED PROTEIN." PROTEIN ENGINEERING 6 (1993): 114-114. Link to Item
  - HEMMINGSEN, JM, RICHARDSON, JS, and RICHARDSON, DC. "A COMMON ARCH STRUCTURE IN BETA SANDWICH PROTEINS - THE TYROSINE TURN." PROTEIN ENGINEERING 6 (1993): 104-104. Link to Item
  - Richardson, JS, Richardson, DC, Tweedy, NB, Gernert, KM, Quinn, TP, Hecht, MH, Erickson, BW, Yan, Y, McClain, RD, and Donlan, ME. "Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992." Biophys J 63, no. 5 (November 1992): 1185-1209. (Review) Link to Item
  - Richardson, DC, and Richardson, JS. "The kinemage: a tool for scientific communication." Protein Science : a Publication of the Protein Society 1, no. 1 (January 1992): 3-9. Full Text
  - Hecht, MH, Richardson, JS, Richardson, DC, and Ogden, RC. "De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence." Science 249, no. 4971 (August 24, 1990): 884-891. Link to Item
  - Harrison, R, and Richardson, D. "Bitewing radiographs of children taken with and without a film-holding device." Dentomaxillofacial Radiology 18, no. 3 (August 1989): 97-99. Full Text
  - Richardson, JS, and Richardson, DC. "The de novo design of protein structures." Trends Biochem Sci 14, no. 7 (July 1989): 304-309. (Review) Link to Item
  - Richardson, JS, and Richardson, DC. "Amino acid preferences for specific locations at the ends of alpha helices." Science (New York, N.Y.) 240, no. 4859 (June 1988): 1648-1652. Full Text
  - Richardson, J, and Richardson, D. "Erratum: Amino acid preferences for specific locations at the ends of α helices (Science (1988) (1648))." Science 242, no. 4886 (1988): 1624--.
  - Richardson, JS, and 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 4, no. 4 (1988): 229-239. Full Text Link to Item
  - McRee, DE, Richardson, DC, Richardson, JS, and Siegel, LM. "The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase." J Biol Chem 261, no. 22 (August 5, 1986): 10277-10281. Link to Item
  - McRee, DE, Richardson, DC, Richardson, JS, and Siegel, LM. "The heme and Fe4S4cluster in the crystallographic structure of Escherichia coli sulfite reductase." Journal of Biological Chemistry 261, no. 22 (January 1, 1986): 10277-10281.
  - McRee, DE, Richardson, JS, and Richardson, DC. "Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli." J Mol Biol 182, no. 3 (April 5, 1985): 467-468. Link to Item
  - Richardson, JS, and Richardson, DC. "Interpretation of electron density maps." Methods Enzymol 115 (1985): 189-206. Link to Item
  - Unson, CG, Erickson, BW, Richardson, DC, and Richardson, JS. "Protein engineering: Design and synthesis of a protein." Federation Proceedings 43, no. 6 (1984): no.-2457.
  - Getzoff, ED, Tainer, JA, Weiner, PK, Kollman, PA, Richardson, JS, and Richardson, DC. "Electrostatic recognition between superoxide and copper, zinc superoxide dismutase." Nature 306, no. 5940 (November 1983): 287-290. Full Text
  - Tainer, JA, Getzoff, ED, Richardson, JS, and Richardson, DC. "Structure and mechanism of copper, zinc superoxide dismutase." Nature 306, no. 5940 (November 1983): 284-287. Full Text
  - Tainer, JA, Getzoff, ED, Beem, KM, Richardson, JS, and Richardson, DC. "Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase." Journal of Molecular Biology 160, no. 2 (September 1982): 181-217. Full Text
  - McRee, DE, and Richardson, DC. "Preliminary X-ray diffraction studies on the hemoprotein subunit of Escherichia coli sulfite reductase." J Mol Biol 154, no. 1 (January 5, 1982): 179-180. Link to Item
  - Taylor, HC, Richardson, DC, Richardson, JS, Wlodawer, A, Komoriya, A, and Chaikes, IM. ""Active" conformation of an inactive semi-synthetic ribonuclease-S." Journal of Molecular Biology 149, no. 2 (June 1981): 313-317. Full Text
  - RICHARDSON, JS, TAINER, JA, and RICHARDSON, DC. "AN ILLUSTRATED MUSEUM OF PROTEIN STRUCTURES." BIOPHYSICAL JOURNAL 32, no. 1 (1980): 211-213. Full Text Link to Item
  - Richardson, JS, Getzoff, ED, and Richardson, DC. "The beta bulge: a common small unit of nonrepetitive protein structure." Proceedings of the National Academy of Sciences of the United States of America 75, no. 6 (June 1978): 2574-2578. Full Text
  - Beem, KM, Richardson, DC, and Rajagopalan, KV. "Metal sites of copper-zinc superoxide dismutase." Biochemistry 16, no. 9 (May 3, 1977): 1930-1936. Link to Item
  - Beem, KM, Richardson, JS, and Richardson, DC. "Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies." J Mol Biol 105, no. 2 (August 5, 1976): 327-332. Link to Item
  - Richardson, JS, Richardson, DC, Thomas, KA, Silverton, EW, and Davies, DR. "Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit." J Mol Biol 102, no. 2 (April 5, 1976): 221-235. Link to Item
  - Richardson, JS, Thomas, KA, and Richardson, DC. "Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase." Biochem Biophys Res Commun 63, no. 4 (April 21, 1975): 986-992. Link to Item
  - Richardson, J, Thomas, KA, Rubin, BH, and 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 72, no. 4 (April 1975): 1349-1353. Link to Item
  - Thomas, KA, Rubin, BH, Bier, CJ, Richardson, JS, and Richardson, DC. "The crystal structure of bovine Cu2+,Zn2+ superoxide dismutase at 5.5-A resolution." J Biol Chem 249, no. 17 (September 10, 1974): 5677-5683. Link to Item
  - Richardson, DC, Bier, CJ, and Richardson, JS. "Two crystal forms of bovine superoxide dismutase." J Biol Chem 247, no. 19 (October 10, 1972): 6368-6369. Link to Item
  - Arnone, A, Bier, CJ, Cotton, FA, Day, VW, Hazen, EE, Richardson, DC, Yonath, A, and Richardson, JS. "A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing." J Biol Chem 246, no. 7 (April 10, 1971): 2302-2316. Link to Item
  - Arnone, A, Bier, CJ, Cotton, FA, Hazen, EE, Richardson, DC, and 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 64, no. 2 (October 1969): 420-427. Link to Item
  - Cotton, FA, and Richardson, DC. "Molecular Structure and Bonding in Diethylenetriaminechromium Tricarbonyl: The Cr(0) and Approximate Mn(0) Radii." Inorganic Chemistry 5, no. 11 (November 1966): 1851-1854. Full Text
  - Cotton, FA, Hazen, EE, and Richardson, DC. "Crystalline extracellular nuclease of Staphylococcus aureus." J Biol Chem 241, no. 19 (October 10, 1966): 4389-4390. Link to Item
  - Haight, GP, Richardson, DC, and Coburn, NH. "A Spectrophotometric Study of Equilibria Involving Mononuclear Chromium(VI) Species in Solutions of Various Acids." Inorganic Chemistry 3, no. 12 (December 1964): 1777-1780. Full Text
- Conference Papers
  - Dicks, E, Teague, JW, Stephens, P, Raine, K, Yates, A, Mattocks, C, Tarpey, P, Butler, A, Menzies, A, Richardson, D, Jenkinson, A, Davies, H, Edkins, S, Forbes, S, Gray, K, Greenman, C, Shepherd, R, Stratton, MR, Futreal, PA, and Wooster, R. "AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes." July 2007. Full Text
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