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Jane S. Richardson - Publications

Affiliations: 
Biochemistry Duke University, Durham, NC 
Area:
3D structures of proteins
Website:
http://www.biochem.duke.edu/modules/biochem_richard_lab/index.php?id=1
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135 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, ... ... Richardson JS, et al. Community recommendations on cryoEM data archiving and validation. Iucrj. PMID 38358351 DOI: 10.1107/S2052252524001246  0.516
2023 Kleywegt GJ, Adams PD, Butcher SJ, Lawson C, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, ... ... Richardson JS, et al. Community recommendations on cryoEM data archiving and validation. Arxiv. PMID 38076521  0.516
2023 Terwilliger TC, Liebschner D, Croll TI, Williams CJ, McCoy AJ, Poon BK, Afonine PV, Oeffner RD, Richardson JS, Read RJ, Adams PD. AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Nature Methods. PMID 38036854 DOI: 10.1038/s41592-023-02087-4  0.511
2023 Richardson JS, Williams CJ, Chen VB, Prisant MG, Richardson DC. The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions. Acta Crystallographica. Section D, Structural Biology. PMID 37921807 DOI: 10.1107/S2059798323008847  0.624
2023 Terwilliger TC, Afonine PV, Liebschner D, Croll TI, McCoy AJ, Oeffner RD, Williams CJ, Poon BK, Richardson JS, Read RJ, Adams PD. Accelerating crystal structure determination with iterative AlphaFold prediction. Acta Crystallographica. Section D, Structural Biology. 79: 234-244. PMID 36876433 DOI: 10.1107/S205979832300102X  0.536
2022 Terwilliger TC, Poon BK, Afonine PV, Schlicksup CJ, Croll TI, Millán C, Richardson JS, Read RJ, Adams PD. Improved AlphaFold modeling with implicit experimental information. Nature Methods. PMID 36266465 DOI: 10.1038/s41592-022-01645-6  0.479
2021 Williams CJ, Richardson DC, Richardson JS. The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. Protein Science : a Publication of the Protein Society. PMID 34779043 DOI: 10.1002/pro.4239  0.628
2021 Richardson JS, Richardson DC, Goodsell DS. Seeing the PDB. The Journal of Biological Chemistry. 100742. PMID 33957126 DOI: 10.1016/j.jbc.2021.100742  0.633
2021 Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, ... ... Richardson JS, et al. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods. PMID 33542514 DOI: 10.1038/s41592-020-01051-w  0.531
2021 Croll TI, Williams CJ, Chen VB, Richardson DC, Richardson JS. Improving SARS-CoV-2 Structures: Peer Review by Early Coordinate Release. Biophysical Journal. PMID 33460600 DOI: 10.1016/j.bpj.2020.12.029  0.649
2020 Croll T, Diederichs K, Fischer F, Fyfe C, Gao Y, Horrell S, Joseph AP, Kandler L, Kippes O, Kirsten F, Müller K, Nolte K, Payne A, Reeves MG, Richardson J, et al. Making the invisible enemy visible. Biorxiv : the Preprint Server For Biology. PMID 33052340 DOI: 10.1101/2020.10.07.307546  0.335
2020 Richardson JS. A new way to see RNAs. Nature Methods. 17: 663-664. PMID 32616927 DOI: 10.1038/S41592-020-0888-7  0.334
2020 Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Crystallographica. Section D, Structural Biology. 76: 51-62. PMID 31909743 DOI: 10.1107/S2059798319015134  0.605
2019 Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC. New Tools in MolProbity Validation: CaBLAM for CryoEM Backbone, UnDowser to Rethink "Waters", and NGL Viewer to Recapture Online 3D Graphics. Protein Science : a Publication of the Protein Society. PMID 31724275 DOI: 10.1002/Pro.3786  0.661
2019 Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, ... Richardson JS, et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallographica. Section D, Structural Biology. 75: 861-877. PMID 31588918 DOI: 10.1107/S2059798319011471  0.706
2019 Williams C, Richardson DC, Richardson JS. A database of high-quality protein residues for reference data, library construction and motif analysis Acta Crystallographica Section a Foundations and Advances. 75: a437-a437. DOI: 10.1107/S0108767319095746  0.631
2019 Sarkar D, Vant J, Shekhar M, Richardson JS, Skeel R, Singharoy A. MDFF Error Analysis: A Tool for Determining Stereochemical and Thermodynamic Correct Structures Biophysical Journal. 116: 140a-141a. DOI: 10.1016/J.Bpj.2018.11.780  0.345
2018 Richardson JS, Williams CJ, Videau LL, Chen VB, Richardson DC. Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale. Journal of Structural Biology. PMID 30107233 DOI: 10.1016/J.Jsb.2018.08.007  0.684
2018 Wang Y, Shekhar M, Thifault D, Williams CJ, Mcgreevy R, Richardson J, Singharoy A, Tajkhorshid E. Constructing Atomic Structural Models into Cryo-EM Densities using Molecular Dynamics - Pros and Cons. Journal of Structural Biology. PMID 30092279 DOI: 10.1016/J.Jsb.2018.08.003  0.396
2018 Richardson JS, Williams CJ, Hintze BJ, Chen VB, Prisant MG, Videau LL, Richardson DC. Model validation: local diagnosis, correction and when to quit. Acta Crystallographica. Section D, Structural Biology. 74: 132-142. PMID 29533239 DOI: 10.1107/S2059798317009834  0.664
2018 Richardson JS, Williams CJ, Videau LL, Richardson DC. Molecular therapy for 2.5–4 Å models: anecdotes and progress from the Cryo-EM Model Challenge Acta Crystallographica Section a Foundations and Advances. 74: a298-a298. DOI: 10.1107/S0108767318097027  0.582
2017 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, ... ... Richardson JS, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Science : a Publication of the Protein Society. PMID 29067766 DOI: 10.1002/Pro.3330  0.809
2017 Hintze BJ, Richardson JS, Richardson DC. Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallographica. Section D, Structural Biology. 73: 852-859. PMID 28994414 DOI: 10.1107/S2059798317013729  0.634
2017 Richardson JS, Videau LL, Williams CJ, Richardson DC. Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. Journal of Molecular Biology. PMID 28336403 DOI: 10.1016/J.Jmb.2017.03.017  0.626
2016 Hintze BJ, Lewis SM, Richardson JS, Richardson DC. MolProbity's Ultimate Rotamer-Library Distributions for Model Validation. Proteins. PMID 27018641 DOI: 10.1002/Prot.25039  0.645
2015 Jain S, Richardson DC, Richardson JS. Computational Methods for RNA Structure Validation and Improvement. Methods in Enzymology. 558: 181-212. PMID 26068742 DOI: 10.1016/Bs.Mie.2015.01.007  0.631
2014 Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Research. 42: 12833-46. PMID 25326328 DOI: 10.1093/Nar/Gku992  0.663
2014 Deis LN, Pemble CW, Qi Y, Hagarman A, Richardson DC, Richardson JS, Oas TG. Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Structure (London, England : 1993). 22: 1467-77. PMID 25295398 DOI: 10.1016/J.Str.2014.08.014  0.646
2014 Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 70: 1104-14. PMID 24699654 DOI: 10.1107/S1399004714001308  0.554
2014 Richardson JS, Richardson DC. Biophysical highlights from 54 years of macromolecular crystallography. Biophysical Journal. 106: 510-25. PMID 24507592 DOI: 10.1016/J.Bpj.2014.01.001  0.646
2014 Hintze B, Zhou H, Al-Hashimi H, Richardson D, Richardson J. Hidden Hoogsteens in the Data Acta Crystallographica Section a Foundations and Advances. 70: C1508-C1508. DOI: 10.1107/S2053273314084915  0.599
2014 Richardson JS. Crystallography - Energetically Innovative at 100 Biophysical Journal. 106: 34a. DOI: 10.1016/J.Bpj.2013.11.261  0.353
2013 Richardson JS, Prisant MG, Richardson DC. Crystallographic model validation: from diagnosis to healing. Current Opinion in Structural Biology. 23: 707-14. PMID 24064406 DOI: 10.1016/J.Sbi.2013.06.004  0.654
2013 Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL. Recommendations of the wwPDB NMR Validation Task Force. Structure (London, England : 1993). 21: 1563-70. PMID 24010715 DOI: 10.1016/J.Str.2013.07.021  0.39
2013 Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics. 42: 265-87. PMID 23451892 DOI: 10.1146/Annurev-Biophys-083012-130253  0.733
2013 Richardson JS, Richardson DC. Doing molecular biophysics: finding, naming, and picturing signal within complexity. Annual Review of Biophysics. 42: 1-28. PMID 23451888 DOI: 10.1146/Annurev-Biophys-083012-130353  0.618
2013 Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods in Enzymology. 523: 87-107. PMID 23422427 DOI: 10.1016/B978-0-12-394292-0.00005-9  0.645
2013 Richardson JS, Richardson DC. Studying and polishing the PDB's macromolecules. Biopolymers. 99: 170-82. PMID 23023928 DOI: 10.1002/Bip.22108  0.677
2013 Hintze BJ, Keedy DA, Richardson DC, Richardson JS. Real Rotamers using Real-Space Correlation Coefficients Biophysical Journal. 104: 547a. DOI: 10.1016/J.Bpj.2012.11.3032  0.642
2013 Williams CJ, Richardson DC, Richardson JS. Through the Ramachandran Haze: Ca-Parameters Reveal Secondary Structure at Low Resolution Biophysical Journal. 104: 19a-20a. DOI: 10.1016/J.Bpj.2012.11.137  0.682
2013 Richardson JS, Richardson DC. The zen of model anomalies - Correct most of them. Treasure the meaningful valid few. Live serenely with the rest! Nato Science For Peace and Security Series a: Chemistry and Biology. 1-10. DOI: 10.1007/978-94-007-6232-9-1  0.542
2012 Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. Plos Computational Biology. 8: e1002629. PMID 22876172 DOI: 10.1371/Journal.Pcbi.1002629  0.68
2012 Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD. Graphical tools for macromolecular crystallography in PHENIX. Journal of Applied Crystallography. 45: 581-586. PMID 22675231 DOI: 10.1107/S0021889812017293  0.765
2012 Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica. Section D, Biological Crystallography. 68: 381-90. PMID 22505258 DOI: 10.1107/S0907444911047834  0.8
2012 Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. Chapter 21.6 MolProbity: all-atom structure validation for macromolecular crystallography International Tables For Crystallography. DOI: 10.1107/97809553602060000884  0.824
2012 Chen VB, Richardson JS, Richardson DC. KiNG and kinemages International Tables For Crystallography. DOI: 10.1107/97809553602060000883  0.674
2011 Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, et al. A new generation of crystallographic validation tools for the protein data bank. Structure (London, England : 1993). 19: 1395-412. PMID 22000512 DOI: 10.1016/J.Str.2011.08.006  0.605
2011 Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, ... Richardson JS, et al. The Phenix software for automated determination of macromolecular structures. Methods (San Diego, Calif.). 55: 94-106. PMID 21821126 DOI: 10.1016/J.Ymeth.2011.07.005  0.805
2011 Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science (New York, N.Y.). 332: 981-4. PMID 21596992 DOI: 10.1126/Science.1202692  0.334
2011 Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology. 405: 607-18. PMID 21073878 DOI: 10.1016/J.Jmb.2010.11.008  0.675
2011 Echols N, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Headd JJ, Hung L-, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, et al. Graphical tools for structure determination and refinement inPHENIX Acta Crystallographica Section a Foundations of Crystallography. 67: C161-C162. DOI: 10.1107/S0108767311096024  0.803
2010 Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Journal of Applied Crystallography. 43: 669-676. PMID 20648263 DOI: 10.1107/S0021889810015608  0.781
2010 Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, ... Richardson JS, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica. Section D, Biological Crystallography. 66: 213-21. PMID 20124702 DOI: 10.1107/S0907444909052925  0.791
2010 Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography. 66: 12-21. PMID 20057044 DOI: 10.1107/S0907444909042073  0.828
2009 Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins. 77: 29-49. PMID 19731372 DOI: 10.1002/Prot.22551  0.797
2009 Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC. Recent developments in phasing and structure refinement for macromolecular crystallography. Current Opinion in Structural Biology. 19: 566-72. PMID 19700309 DOI: 10.1016/J.Sbi.2009.07.014  0.708
2009 Tress ML, Ezkurdia I, Richardson JS. Target domain definition and classification in CASP8. Proteins. 77: 10-7. PMID 19603487 DOI: 10.1002/Prot.22497  0.38
2009 Block JN, Zielinski DJ, Chen VB, Davis IW, Vinson EC, Brady R, Richardson JS, Richardson DC. KinImmerse: Macromolecular VR for NMR ensembles. Source Code For Biology and Medicine. 4: 3. PMID 19222844 DOI: 10.1186/1751-0473-4-3  0.625
2009 Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. Journal of Structural and Functional Genomics. 10: 83-93. PMID 19002604 DOI: 10.1007/S10969-008-9045-8  0.804
2008 Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Algorithm for backrub motions in protein design. Bioinformatics (Oxford, England). 24: i196-204. PMID 18586714 DOI: 10.1093/bioinformatics/btn169  0.615
2008 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, et al. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). Rna (New York, N.Y.). 14: 465-81. PMID 18192612 DOI: 10.1261/Rna.657708  0.793
2008 Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. Journal of Mathematical Biology. 56: 253-78. PMID 17401565 DOI: 10.1007/S00285-007-0082-X  0.645
2007 Gerwe B, Kelley LL, Dillard BD, Lai T, Liu ZJ, Tempel W, Chen L, Habel J, Lee D, Jenney FE, Sugar FJ, Richardson JS, Richardson DC, Newton MG, Wang BC, 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. Journal of Structural and Functional Genomics. 8: 1-10. PMID 17932790 DOI: 10.1007/S10969-007-9026-3  0.609
2007 Kelley LL, Dillard BD, Tempel W, Chen L, Shaw N, Lee D, Newton MG, Sugar FJ, Jenney FE, Lee HS, Shah C, Poole FL, Adams MW, Richardson JS, Richardson DC, et al. Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 63: 549-52. PMID 17620707 DOI: 10.1107/S1744309107024049  0.674
2007 Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research. 35: W375-83. PMID 17452350 DOI: 10.1093/Nar/Gkm216  0.662
2006 Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 12: 533-41. PMID 16484377 DOI: 10.1261/Rna.2343206  0.325
2006 Davis IW, Arendall WB, Richardson DC, Richardson JS. The backrub motion: how protein backbone shrugs when a sidechain dances. Structure (London, England : 1993). 14: 265-74. PMID 16472746 DOI: 10.1016/J.Str.2005.10.007  0.646
2006 Furey W, Cowtan KD, Zhang KYJ, Main P, Brunger AT, Adams PD, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-, Pannu NS, Read RJ, Rice LM, Simonson T, Tronrud DE, ... ... Richardson JS, et al. Programs and program systems in wide use International Tables For Crystallography. 695-743. DOI: 10.1107/97809553602060000724  0.62
2005 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, et al. Away from the edge II: in-house Se-SAS phasing with chromium radiation. Acta Crystallographica. Section D, Biological Crystallography. 61: 960-6. PMID 15983419 DOI: 10.1107/S0907444905010644  0.631
2005 Arendall WB, Tempel W, Richardson JS, Zhou W, Wang S, Davis IW, Liu ZJ, Rose JP, Carson WM, Luo M, Richardson DC, Wang BC. A test of enhancing model accuracy in high-throughput crystallography. Journal of Structural and Functional Genomics. 6: 1-11. PMID 15965733 DOI: 10.1007/S10969-005-3138-4  0.682
2005 Liu ZJ, 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 SH, Zhou W, ... ... Richardson JS, et al. The high-throughput protein-to-structure pipeline at SECSG. Acta Crystallographica. Section D, Biological Crystallography. 61: 679-84. PMID 15930619 DOI: 10.1107/S0907444905013132  0.65
2005 Murray LJ, Richardson JS, Arendall WB, Richardson DC. RNA backbone rotamers--finding your way in seven dimensions. Biochemical Society Transactions. 33: 485-7. PMID 15916548 DOI: 10.1042/Bst0330485  0.635
2005 Butterfoss GL, Richardson JS, Hermans J. Protein imperfections: separating intrinsic from extrinsic variation of torsion angles. Acta Crystallographica. Section D, Biological Crystallography. 61: 88-98. PMID 15608380 DOI: 10.1107/S0907444904027325  0.395
2005 Booth D, Bateman RC, Sirochman R, Richardson DC, Richardson JS, Weiner SW, Farwell M, Putnam-Evans C. Assessment of molecular construction in undergraduate biochemistry Journal of Chemical Education. 82: 1854-1858. DOI: 10.1021/Ed082P1854  0.566
2004 Tempel W, Liu ZJ, Schubot FD, Shah A, Weinberg MV, Jenney FE, Arendall WB, Adams MW, Richardson JS, Richardson DC, Rose JP, Wang BC. Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. Proteins. 57: 878-82. PMID 15468318 DOI: 10.1002/Prot.20280  0.589
2004 Richardson JS. The protein surface is a moving target. Structure (London, England : 1993). 12: 912-3. PMID 15274911 DOI: 10.1016/J.Str.2004.05.002  0.334
2004 Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Research. 32: W615-9. PMID 15215462 DOI: 10.1093/Nar/Gkh398  0.645
2004 Videau LL, Arendall WB, Richardson JS. The cis-Pro touch-turn: a rare motif preferred at functional sites. Proteins. 56: 298-309. PMID 15211513 DOI: 10.1002/Prot.20101  0.373
2004 Wales TE, Richardson JS, Fitzgerald MC. Facile chemical synthesis and equilibrium unfolding properties of CopG. Protein Science : a Publication of the Protein Society. 13: 1918-26. PMID 15169951 DOI: 10.1110/Ps.04671804  0.33
2004 Kapp GT, Richardson JS, Oas TG. Kinetic role of helix caps in protein folding is context-dependent. Biochemistry. 43: 3814-23. PMID 15049688 DOI: 10.1021/Bi035683K  0.313
2003 Richardson JS, Bryan WA, Richardson DC. New tools and data for improving structures, using all-atom contacts. Methods in Enzymology. 374: 385-412. PMID 14696383 DOI: 10.1016/S0076-6879(03)74018-X  0.687
2003 Murray LJ, Arendall WB, Richardson DC, Richardson JS. RNA backbone is rotameric. Proceedings of the National Academy of Sciences of the United States of America. 100: 13904-9. PMID 14612579 DOI: 10.1073/Pnas.1835769100  0.626
2003 Richardson JS. All-atom contacts: a new approach to structure validation. Methods of Biochemical Analysis. 44: 305-20. PMID 12647392 DOI: 10.1002/0471721204.Ch15  0.356
2003 Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 50: 437-50. PMID 12557186 DOI: 10.1002/Prot.10286  0.675
2002 Richardson JS, Richardson DC. Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proceedings of the National Academy of Sciences of the United States of America. 99: 2754-9. PMID 11880627 DOI: 10.1073/Pnas.052706099  0.598
2002 Bateman RC, Booth D, Sirochman R, Richardson J, Richardson D. Teaching and assessing three-dimensional molecular literacy in undergraduate biochemistry Journal of Chemical Education. 79: 551. DOI: 10.1021/Ed079P551  0.634
2002 Richardson DC, Richardson JS. Teaching molecular 3-D literacy Biochemistry and Molecular Biology Education. 30: 21-26. DOI: 10.1002/Bmb.2002.494030010005  0.544
2001 Grell D, Richardson JS, Mutter M. Protein design and folding: template trapping of self-assembled helical bundles. Journal of Peptide Science : An Official Publication of the European Peptide Society. 7: 146-51. PMID 11297350 DOI: 10.1002/Psc.308  0.35
2000 Grell D, Richardson JS, Richardson DC, Mutter M. SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics. Journal of Molecular Graphics & Modelling. 18: 290-8, 309-10. PMID 11021545 DOI: 10.1016/S1093-3263(00)00049-8  0.676
2000 Richardson JS. Early ribbon drawings of proteins. Nature Structural Biology. 7: 624-5. PMID 10932243 DOI: 10.1038/77912  0.381
2000 Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins. 40: 389-408. PMID 10861930 DOI: 10.1002/1097-0134(20000815)40:3<389::Aid-Prot50>3.0.Co;2-2  0.649
1999 Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. Journal of Molecular Biology. 285: 1735-47. PMID 9917408 DOI: 10.1006/Jmbi.1998.2401  0.646
1999 Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Journal of Molecular Biology. 285: 1711-33. PMID 9917407 DOI: 10.1006/Jmbi.1998.2400  0.689
1999 Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proceedings of the National Academy of Sciences of the United States of America. 96: 400-5. PMID 9892645 DOI: 10.1073/pnas.96.2.400  0.58
1996 Gernert KM, Thomas BD, Plurad JC, Richardson JS, Richardson DC, Bergman LD. Puzzle pieces defined: locating common packing units in tertiary protein contacts. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 331-49. PMID 9390242  0.625
1995 Gernert KM, Surles MC, Labean TH, Richardson JS, Richardson DC. The Alacoil: a very tight, antiparallel coiled-coil of helices. Protein Science : a Publication of the Protein Society. 4: 2252-60. PMID 8563621 DOI: 10.1002/Pro.5560041102  0.628
1995 Bergman LD, Richardson JS, Richardson DC. An algorithm for smoothly tessellating beta-sheet structures in proteins. Journal of Molecular Graphics. 13: 36-45, 58. PMID 7794833 DOI: 10.1016/0263-7855(94)00003-B  0.63
1994 Richardson DC, Richardson JS. Kinemages--simple macromolecular graphics for interactive teaching and publication. Trends in Biochemical Sciences. 19: 135-8. PMID 8203021 DOI: 10.1016/0968-0004(94)90207-0  0.557
1994 Quinn TP, Tweedy NB, Williams RW, Richardson JS, Richardson DC. Betadoublet: de novo design, synthesis, and characterization of a beta-sandwich protein. Proceedings of the National Academy of Sciences of the United States of America. 91: 8747-51. PMID 8090717 DOI: 10.1073/Pnas.91.19.8747  0.634
1994 Surles MC, Richardson JS, Richardson DC, Brooks FP. Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system. Protein Science : a Publication of the Protein Society. 3: 198-210. PMID 8003957 DOI: 10.1002/Pro.5560030205  0.648
1994 Richardson JS. Introduction: Protein motifs Faseb Journal. 8: 1237-1239. PMID 8001735 DOI: 10.1096/Fasebj.8.15.8001735  0.317
1994 Hemmingsen JM, Gernert KM, Richardson JS, Richardson DC. The tyrosine corner: a feature of most Greek key beta-barrel proteins. Protein Science : a Publication of the Protein Society. 3: 1927-37. PMID 7703839 DOI: 10.1002/Pro.5560031104  0.62
1993 Bergman LD, Richardson JS, Richardson DC, Brooks FP. VIEW an exploratory molecular visualization system with user-definable interaction sequences Proceedings of the 20th Annual Conference On Computer Graphics and Interactive Techniques, Siggraph 1993. 117-126. DOI: 10.1145/166117.166132  0.53
1993 Gernert RM, Richardson JS, Richardson DC. Structural characteristics of felix, a designed protein Protein Engineering, Design and Selection. 6: 114. DOI: 10.1093/Protein/6.Supplement.114-A  0.641
1993 Hemmingsen JM, Richardson JS, Richardson DC. A common arch structure in beta sandwich proteins: The tyrosine turn Protein Engineering, Design and Selection. 6: 104. DOI: 10.1093/Protein/6.Supplement.104  0.625
1992 Richardson JS, Richardson DC, Tweedy NB, Gernert KM, Quinn TP, Hecht MH, Erickson BW, Yan Y, McClain RD, Donlan ME. Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992. Biophysical Journal. 63: 1185-209. PMID 1477272  0.723
1992 Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Science : a Publication of the Protein Society. 1: 3-9. PMID 1304880 DOI: 10.1002/Pro.5560010102  0.582
1990 Hecht MH, Richardson JS, Richardson DC, Ogden RC. De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science (New York, N.Y.). 249: 884-91. PMID 2392678 DOI: 10.1126/Science.2392678  0.719
1989 Richardson JS, Richardson DC. The de novo design of protein structures. Trends in Biochemical Sciences. 14: 304-9. PMID 2672455 DOI: 10.1016/0968-0004(89)90070-4  0.593
1988 Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science (New York, N.Y.). 240: 1648-52. PMID 3381086 DOI: 10.1126/Science.3381086  0.595
1988 Richardson JS, Richardson DC. Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal. Proteins. 4: 229-39. PMID 2855370 DOI: 10.1002/Prot.340040402  0.603
1986 McRee DE, Richardson DC, Richardson JS, Siegel LM. The heme and Fe4S4 cluster in the crystallographic structure of Escherichia coli sulfite reductase. The Journal of Biological Chemistry. 261: 10277-81. PMID 3525540  0.533
1985 Richardson JS. Describing patterns of protein tertiary structure Methods in Enzymology. 115: 341-358. PMID 4079792 DOI: 10.1016/0076-6879(85)15025-1  0.388
1985 McRee DE, Richardson JS, Richardson DC. Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli. Journal of Molecular Biology. 182: 467-8. PMID 3892013 DOI: 10.1016/0022-2836(85)90205-0  0.594
1985 Richardson JS. Schematic drawings of protein structures Methods in Enzymology. 115: 359-380. PMID 3853075 DOI: 10.1016/0076-6879(85)15026-3  0.357
1985 Richardson JS, Richardson DC. Interpretation of electron density maps. Methods in Enzymology. 115: 189-206. PMID 3841180 DOI: 10.1016/0076-6879(85)15016-0  0.647
1985 Richardson JS. Protein structure: A new twist for hairpin turns Nature. 316: 102-103. DOI: 10.1038/316102B0  0.413
1984 Unson CG, Erickson BW, Richardson DC, Richardson JS. Protein engineering: Design and synthesis of a protein Federation Proceedings. 43: no. 2457.  0.546
1983 Getzoff ED, Tainer JA, Weiner PK, Kollman PA, Richardson JS, Richardson DC. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature. 306: 287-90. PMID 6646211 DOI: 10.1038/306287A0  0.724
1983 Tainer JA, Getzoff ED, Richardson JS, Richardson DC. Structure and mechanism of copper, zinc superoxide dismutase. Nature. 306: 284-7. PMID 6316150 DOI: 10.1038/306284A0  0.732
1982 Tainer JA, Getzoff ED, Beem KM, Richardson JS, Richardson DC. Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. Journal of Molecular Biology. 160: 181-217. PMID 7175933 DOI: 10.1016/0022-2836(82)90174-7  0.745
1981 Taylor HC, Richardson DC, Richardson JS, Wlodawer A, Komoriya A, Chaikes IM. "Active" conformation of an inactive semi-synthetic ribonuclease-S. Journal of Molecular Biology. 149: 313-7. PMID 7310884 DOI: 10.1016/0022-2836(81)90305-3  0.647
1981 Richardson JS. The anatomy and taxonomy of protein structure. Advances in Protein Chemistry. 34: 167-339. PMID 7020376 DOI: 10.1016/S0065-3233(08)60520-3  0.414
1980 Richardson JS, Tainer JA, Richardson DC. An illustrated museum of protein structures. Biophysical Journal. 32: 211-3. PMID 19431356 DOI: 10.1016/S0006-3495(80)84934-4  0.721
1979 Richardson JS. The singly-wound parallel beta barrel: a proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase. Biochemical and Biophysical Research Communications. 90: 285-90. PMID 496979 DOI: 10.1016/0006-291X(79)91622-X  0.307
1979 Kimball MR, Sato A, Richardson JS, Rosen LS, Low BW. Molecular conformation of erabutoxin b; atomic coordinates at 2.5 A resolution. Biochemical and Biophysical Research Communications. 88: 950-9. PMID 465091 DOI: 10.1016/0006-291X(79)91500-6  0.34
1978 Richardson JS, Getzoff ED, Richardson DC. The beta bulge: a common small unit of nonrepetitive protein structure. Proceedings of the National Academy of Sciences of the United States of America. 75: 2574-8. PMID 275827 DOI: 10.1073/Pnas.75.6.2574  0.687
1977 Richardson JS. beta-Sheet topology and the relatedness of proteins. Nature. 268: 495-500. PMID 329147 DOI: 10.1038/268495A0  0.359
1976 Richardson JS, Richardson DC, Thomas KA, Silverton EW, Davies DR. Similarity of three-dimensional structure between the immunoglobulin domain and the copper, zinc superoxide dismutase subunit. Journal of Molecular Biology. 102: 221-35. PMID 1271464 DOI: 10.1016/S0022-2836(76)80050-2  0.641
1976 Low BW, Preston HS, Sato A, Rosen LS, Searl JE, Rudko AD, Richardson JS. Three dimensional structure of erabutoxin b neurotoxic protein: inhibitor of acetylcholine receptor. Proceedings of the National Academy of Sciences of the United States of America. 73: 2991-4. PMID 1067597 DOI: 10.1073/Pnas.73.9.2991  0.366
1976 Beem KM, Richardson JS, Richardson DC. Manganese superoxide dismutases from Escherichia coli and from yeast mitochondria: preliminary x-ray crystallographic studies. Journal of Molecular Biology. 105: 327-32. PMID 787536 DOI: 10.1016/0022-2836(76)90115-7  0.569
1976 Richardson JS. Handedness of crossover connections in beta sheets. Proceedings of the National Academy of Sciences of the United States of America. 73: 2619-23. PMID 183204 DOI: 10.1073/Pnas.73.8.2619  0.342
1975 Richardson JS, Thomas KA, Richardson DC. Alpha-carbon coordinates for bovine Cu,Zn superoxide dismutase. Biochemical and Biophysical Research Communications. 63: 986-92. PMID 1169067 DOI: 10.1016/0006-291X(75)90666-X  0.595
1975 Richardson J, Thomas KA, Rubin BH, Richardson DC. Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands. Proceedings of the National Academy of Sciences of the United States of America. 72: 1349-53. PMID 1055410 DOI: 10.1073/Pnas.72.4.1349  0.615
1969 Arnone A, Bier CJ, Cotton FA, Hazen EE, Richardson DC, Richardson JS. The extracellular nuclease of Staphylococcus aureus: structures of the native enzyme and an enzyme-inhibitor complex at 4 A resolution. Proceedings of the National Academy of Sciences of the United States of America. 64: 420-7. PMID 5261023 DOI: 10.1073/Pnas.64.2.420  0.62
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