Jane Richardson

Summary

Affiliation: Duke University Medical Center
Country: USA

Publications

  1. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
  2. doi request reprint Biophysical highlights from 54 years of macromolecular crystallography
    Jane S Richardson
    Biochemistry Department, Duke University, Durham, North Carolina Electronic address
    Biophys J 106:510-25. 2014
  3. pmc Crystallographic model validation: from diagnosis to healing
    Jane S Richardson
    Department of Biochemistry, Duke University, 132 Nanaline Duke Bldg, DUMC 3711, Durham, NC 27710, USA Electronic address
    Curr Opin Struct Biol 23:707-14. 2013
  4. pmc Studying and polishing the PDB's macromolecules
    Jane S Richardson
    Department of Biochemistry, Duke University, Durham, North Carolina
    Biopolymers 99:170-82. 2013
  5. pmc KinImmerse: Macromolecular VR for NMR ensembles
    Jeremy N Block
    Biochemistry Department, Duke University Medical Center, Durham, NC 27710, USA
    Source Code Biol Med 4:3. 2009
  6. pmc RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
    Jane S Richardson
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710 3711, USA
    RNA 14:465-81. 2008
  7. pmc Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation
    Jane S Richardson
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Proc Natl Acad Sci U S A 99:2754-9. 2002
  8. pmc Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place
    Jeffrey J Headd
    Department of Biochemistry, Duke University Medical Center, 211 Nanaline Duke Building, 3711 DUMC, Durham, NC 27710, USA
    J Struct Funct Genomics 10:83-93. 2009
  9. pmc The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models
    Daniel A Keedy
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    Proteins 77:29-49. 2009
  10. pmc MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Nucleic Acids Res 32:W615-9. 2004

Collaborators

Detail Information

Publications29

  1. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    ..This service is available free to all users at http://molprobity.biochem.duke.edu...
  2. doi request reprint Biophysical highlights from 54 years of macromolecular crystallography
    Jane S Richardson
    Biochemistry Department, Duke University, Durham, North Carolina Electronic address
    Biophys J 106:510-25. 2014
    ..Chronological by publication of the earliest solved structure, each illustrated entry briefly describes key concepts or methods new at the time and key later work leveraged by knowledge of the three-dimensional atomic structure...
  3. pmc Crystallographic model validation: from diagnosis to healing
    Jane S Richardson
    Department of Biochemistry, Duke University, 132 Nanaline Duke Bldg, DUMC 3711, Durham, NC 27710, USA Electronic address
    Curr Opin Struct Biol 23:707-14. 2013
    ....
  4. pmc Studying and polishing the PDB's macromolecules
    Jane S Richardson
    Department of Biochemistry, Duke University, Durham, North Carolina
    Biopolymers 99:170-82. 2013
    ..2012 Wiley Periodicals, Inc. Biopolymers 99: 170-182, 2013...
  5. pmc KinImmerse: Macromolecular VR for NMR ensembles
    Jeremy N Block
    Biochemistry Department, Duke University Medical Center, Durham, NC 27710, USA
    Source Code Biol Med 4:3. 2009
    ..In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case...
  6. pmc RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
    Jane S Richardson
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710 3711, USA
    RNA 14:465-81. 2008
    ..The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs...
  7. pmc Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation
    Jane S Richardson
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Proc Natl Acad Sci U S A 99:2754-9. 2002
    ..amp; Hecht, M. H. (2002) Proc. Natl. Acad. Sci. USA 99, 2760-2765] makes use of the inward-pointing charge strategy with great success, turning highly aggregated beta-sandwich designs into soluble monomers...
  8. pmc Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place
    Jeffrey J Headd
    Department of Biochemistry, Duke University Medical Center, 211 Nanaline Duke Building, 3711 DUMC, Durham, NC 27710, USA
    J Struct Funct Genomics 10:83-93. 2009
    ..A fully automated method called "Autofix" identifies such errors for Leu, Val, Thr, and Arg and corrects over one third of them, using MolProbity validation criteria and Coot real-space refinement of rotamers...
  9. pmc The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models
    Daniel A Keedy
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
    Proteins 77:29-49. 2009
    ..Predictor groups excelled at different aspects, highlighting the diversity of current methodologies. However, good full-model scores correlate robustly with high Calpha accuracy...
  10. pmc MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Nucleic Acids Res 32:W615-9. 2004
    ..This service is available free to all users at http://kinemage.biochem.duke.edu...
  11. ncbi request reprint All-atom contacts: a new approach to structure validation
    Jane S Richardson
    Department of Biochemistry, Duke University, Durham, NC, USA
    Methods Biochem Anal 44:305-20. 2003
  12. ncbi request reprint The backrub motion: how protein backbone shrugs when a sidechain dances
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
    Structure 14:265-74. 2006
    ..For large sidechain changes in protein dynamics or for single mutations, backrubs allow backbone accommodation while maintaining H bonds and ideal geometry...
  13. pmc RNA backbone is rotameric
    Laura J W Murray
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Proc Natl Acad Sci U S A 100:13904-9. 2003
    ..The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures...
  14. ncbi request reprint A test of enhancing model accuracy in high-throughput crystallography
    W Bryan Arendall
    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710 3711, USA
    J Struct Funct Genomics 6:1-11. 2005
    ..The ease and effectiveness of this technique shows that macromolecular crystal structures from either traditional or high-throughput determinations can feasibly reach a new level of excellence in conformational accuracy and reliability...
  15. ncbi request reprint New tools and data for improving structures, using all-atom contacts
    Jane S Richardson
    Department of Biochemistry, Duke University, Duke Building, Durham, North Carolina 27708, USA
    Methods Enzymol 374:385-412. 2003
  16. pmc MolProbity: all-atom structure validation for macromolecular crystallography
    Vincent B Chen
    Department of Biochemistry, Duke University, Durham, NC 27710, USA
    Acta Crystallogr D Biol Crystallogr 66:12-21. 2010
    ....
  17. ncbi request reprint Kinetic role of helix caps in protein folding is context-dependent
    Gregory T Kapp
    Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
    Biochemistry 43:3814-23. 2004
    ..The accelerated folding rates could result from helix stabilization without invoking a specific role for N-caps in the folding reaction...
  18. pmc Algorithm for backrub motions in protein design
    Ivelin Georgiev
    Department of Computer Science, Duke University, Durham, NC 27708, USA
    Bioinformatics 24:i196-204. 2008
    ....
  19. pmc Facile chemical synthesis and equilibrium unfolding properties of CopG
    Thomas E Wales
    Department of Chemistry, Box 90346, Duke University, Durham, NC 27708 0346, USA
    Protein Sci 13:1918-26. 2004
    ..Using this model, DeltaG(f) and m-values of -13.42 +/- 0.04 kcal/mole dimer and 1.92 +/- 0.01 kcal/(mole M) were calculated for CopG...
  20. ncbi request reprint The cis-Pro touch-turn: a rare motif preferred at functional sites
    Lizbeth L Videau
    Department of Biochemistry, Duke University, Durham, North Carolina 27710 3711, USA
    Proteins 56:298-309. 2004
    ..In analyzing the conservation patterns of these 3D motifs, new methods for in-depth quality evaluation of the structural bioinformatic data are employed to distinguish between significant exceptions and errors..
  21. pmc Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution
    Laura Lee Clancy Kelley
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:549-52. 2007
    ..0% and R(free) of 24.0%. The refined structure shows some structural similarity to a wedge-shaped domain observed in the structure of the major capsid protein from bacteriophage HK97, suggesting that PF0899 may be a structural protein...
  22. ncbi request reprint Structure validation by Calpha geometry: phi,psi and Cbeta deviation
    Simon C Lovell
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 50:437-50. 2003
    ..To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage)...
  23. ncbi request reprint The protein surface is a moving target
    Jane S Richardson
    Structure 12:912-3. 2004
  24. ncbi request reprint Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin
    Wolfram Tempel
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
    Proteins 57:878-82. 2004
  25. ncbi request reprint Protein imperfections: separating intrinsic from extrinsic variation of torsion angles
    Glenn L Butterfoss
    Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599 7260, USA
    Acta Crystallogr D Biol Crystallogr 61:88-98. 2005
    ....
  26. ncbi request reprint The high-throughput protein-to-structure pipeline at SECSG
    Zhi Jie Liu
    Southeast Collaboratory for Structural Genomics, Department of Biochechemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Acta Crystallogr D Biol Crystallogr 61:679-84. 2005
    ..Details of the various procedures in the pipeline for protein crystallization, target salvaging, data collection/processing and high-throughput structure determination/validation, as well as some examples, are described...
  27. pmc The RNA Ontology Consortium: an open invitation to the RNA community
    Neocles B Leontis
    RNA 12:533-41. 2006
    ....
  28. ncbi request reprint 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
    Brian Gerwe
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Davison Life Science Complex, Athens, GA 30602, USA
    J Struct Funct Genomics 8:1-10. 2007
    ..The related PF1090-containing operon is unaffected by cold-shock and is independently regulated...
  29. ncbi request reprint Away from the edge II: in-house Se-SAS phasing with chromium radiation
    Hao Xu
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30605, USA
    Acta Crystallogr D Biol Crystallogr 61:960-6. 2005
    ..The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography...

Research Grants9

  1. All-Atom Contact Analysis In Improving Structure Quality
    Jane Richardson; Fiscal Year: 2002
    ..abstract_text> ..
  2. Inverse Kinematics, Sterics & Data - To Fit RNA Backbone
    Jane Richardson; Fiscal Year: 2007
    ....
  3. "Low-Resolution Interiors & Interfaces Can Achieve High-Resolution Accuracy"
    Jane S Richardson; Fiscal Year: 2010
    ..The proposed research if successful will move that critical tipping point out to larger structures and complexes which are the real machinery of cellular biology and a key application point for molecular medicine. ..
  4. Inverse Kinematics, Sterics & Data - To Fit RNA Backbone
    Jane Richardson; Fiscal Year: 2009
    ....