Jane RichardsonSummaryAffiliation: Duke University Medical Center Country: USA Publications
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Publications
MolProbity: all-atom contacts and structure validation for proteins and nucleic acidsIan 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...- Studying and polishing the PDB's macromoleculesJane S Richardson
Department of Biochemistry, Duke University, Durham, North Carolina
Biopolymers 99:170-82. 2013..2012 Wiley Periodicals, Inc. Biopolymers 99: 170-182, 2013... - KinImmerse: Macromolecular VR for NMR ensemblesJeremy 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... - 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... - Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregationJane 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... - The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy modelsDaniel 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... - Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their placeJeffrey 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... 
All-atom contacts: a new approach to structure validationJane S Richardson
Department of Biochemistry, Duke University, Durham, NC, USA
Methods Biochem Anal 44:305-20. 2003- MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexesIan 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... - The backrub motion: how protein backbone shrugs when a sidechain dancesIan 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... - New tools and data for improving structures, using all-atom contactsJane S Richardson
Department of Biochemistry, Duke University, Duke Building, Durham, North Carolina 27708, USA
Methods Enzymol 374:385-412. 2003 - RNA backbone is rotamericLaura 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... - A test of enhancing model accuracy in high-throughput crystallographyW 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... - MolProbity: all-atom structure validation for macromolecular crystallographyVincent B Chen
Department of Biochemistry, Duke University, Durham, NC 27710, USA
Acta Crystallogr D Biol Crystallogr 66:12-21. 2010.... - Kinetic role of helix caps in protein folding is context-dependentGregory 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... - Facile chemical synthesis and equilibrium unfolding properties of CopGThomas 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... - Algorithm for backrub motions in protein designIvelin Georgiev
Department of Computer Science, Duke University, Durham, NC 27708, USA
Bioinformatics 24:i196-204. 2008.... - The cis-Pro touch-turn: a rare motif preferred at functional sitesLizbeth 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.. - Structure validation by Calpha geometry: phi,psi and Cbeta deviationSimon 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)... - 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 archaeonBrian 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... - Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolutionLaura 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... - The protein surface is a moving targetJane S Richardson
Structure 12:912-3. 2004 - The RNA Ontology Consortium: an open invitation to the RNA communityNeocles B Leontis
RNA 12:533-41. 2006.... - Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrinWolfram Tempel
Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
Proteins 57:878-82. 2004 - Away from the edge II: in-house Se-SAS phasing with chromium radiationHao 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... - Protein imperfections: separating intrinsic from extrinsic variation of torsion anglesGlenn 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.... - The high-throughput protein-to-structure pipeline at SECSGZhi 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...
Research Grants
- All-Atom Contact Analysis In Improving Structure QualityJane Richardson; Fiscal Year: 2002..abstract_text> ..
- Inverse Kinematics, Sterics & Data - To Fit RNA BackboneJane Richardson; Fiscal Year: 2007....
- "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. ..
- Inverse Kinematics, Sterics & Data - To Fit RNA BackboneJane Richardson; Fiscal Year: 2009....