R J Read

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc Crystallography: crystallographic evidence for deviating C3b structure
    Bert J C Janssen
    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
    Nature 448:E1-2; discussion E2-3. 2007
  2. pmc How changes in affinity of corticosteroid-binding globulin modulate free cortisol concentration
    Wee Lee Chan
    Department of Hematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
    J Clin Endocrinol Metab 98:3315-22. 2013
  3. pmc Intensity statistics in the presence of translational noncrystallographic symmetry
    Randy J Read
    Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 0XY, England
    Acta Crystallogr D Biol Crystallogr 69:176-83. 2013
  4. pmc A new generation of crystallographic validation tools for the protein data bank
    Randy J Read
    CIMR, University of Cambridge, Cambridge CB2 0XY, UK
    Structure 19:1395-412. 2011
  5. pmc Using SAD data in Phaser
    Randy J Read
    CIMR Haematology, University of Cambridge, Wellcome Trust MRC Building, Cambridge, England
    Acta Crystallogr D Biol Crystallogr 67:338-44. 2011
  6. pmc Case-controlled structure validation
    Randy J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Cambridge, England
    Acta Crystallogr D Biol Crystallogr 65:140-7. 2009
  7. ncbi request reprint Assessment of CASP7 predictions in the high accuracy template-based modeling category
    Randy J Read
    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Proteins 69:27-37. 2007
  8. ncbi request reprint Detecting outliers in non-redundant diffraction data
    R J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 55:1759-64. 1999
  9. ncbi request reprint Pushing the boundaries of molecular replacement with maximum likelihood
    R J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 57:1373-82. 2001
  10. ncbi request reprint New ways of looking at experimental phasing
    Randy J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 59:1891-902. 2003

Collaborators

Detail Information

Publications32

  1. pmc Crystallography: crystallographic evidence for deviating C3b structure
    Bert J C Janssen
    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
    Nature 448:E1-2; discussion E2-3. 2007
    ..Our findings therefore call into question the crystal structure for C3b reported by Ajees et al....
  2. pmc How changes in affinity of corticosteroid-binding globulin modulate free cortisol concentration
    Wee Lee Chan
    Department of Hematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
    J Clin Endocrinol Metab 98:3315-22. 2013
    ..We show how CBG binding affinity can vary to give changes in free cortisol concentration in a physiologically relevant range...
  3. pmc Intensity statistics in the presence of translational noncrystallographic symmetry
    Randy J Read
    Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 0XY, England
    Acta Crystallogr D Biol Crystallogr 69:176-83. 2013
    ....
  4. pmc A new generation of crystallographic validation tools for the protein data bank
    Randy J Read
    CIMR, University of Cambridge, Cambridge CB2 0XY, UK
    Structure 19:1395-412. 2011
    ..Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators...
  5. pmc Using SAD data in Phaser
    Randy J Read
    CIMR Haematology, University of Cambridge, Wellcome Trust MRC Building, Cambridge, England
    Acta Crystallogr D Biol Crystallogr 67:338-44. 2011
    ..These maps are more sensitive than conventional model-phased anomalous difference Fouriers and the iterative completion algorithm is able to find a significantly larger number of convincing sites...
  6. pmc Case-controlled structure validation
    Randy J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Cambridge, England
    Acta Crystallogr D Biol Crystallogr 65:140-7. 2009
    ..In both cases, once factors influencing quality have been controlled in the comparison, there is little evidence for a systematic difference in quality...
  7. ncbi request reprint Assessment of CASP7 predictions in the high accuracy template-based modeling category
    Randy J Read
    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
    Proteins 69:27-37. 2007
    ..However, when there is already a good template, few of the models are better for the purpose of molecular replacement...
  8. ncbi request reprint Detecting outliers in non-redundant diffraction data
    R J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 55:1759-64. 1999
    ..This captures mostly the excessively strong reflections, which dominate the features of electron-density maps or, even more so, Patterson maps. The outlier rejection tests have been implemented in a program, Outliar...
  9. ncbi request reprint Pushing the boundaries of molecular replacement with maximum likelihood
    R J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 57:1373-82. 2001
    ..Tests in a new molecular-replacement program, Beast, show that the likelihood-based targets are more sensitive and more accurate than previous targets. The new multiple-model likelihood function has a dramatic impact on success...
  10. ncbi request reprint New ways of looking at experimental phasing
    Randy J Read
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 59:1891-902. 2003
    ..However, the new formulation makes the necessary assumptions more explicit and points the way to improving phasing using both isomorphous and anomalous differences...
  11. pmc Experimental phasing: best practice and pitfalls
    Airlie J McCoy
    Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 OXY, England
    Acta Crystallogr D Biol Crystallogr 66:458-69. 2010
    ....
  12. pmc A redox switch in angiotensinogen modulates angiotensin release
    Aiwu Zhou
    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
    Nature 468:108-11. 2010
    ....
  13. doi request reprint The S-to-R transition of corticosteroid-binding globulin and the mechanism of hormone release
    Aiwu Zhou
    Department of Haematology and Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
    J Mol Biol 380:244-51. 2008
    ..The change in the hormone binding affinity results from a change in the flexibility or plasticity of the connecting loop, which modulates the configuration of the binding site...
  14. pmc Structural mechanism for the carriage and release of thyroxine in the blood
    Aiwu Zhou
    Departments of Haematology and Medicine, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, United Kingdom
    Proc Natl Acad Sci U S A 103:13321-6. 2006
    ..The complexity and ready triggering of this conformational mechanism strongly indicates that TBG has evolved to allow a modulated and targeted delivery of thyroxine to the tissues...
  15. ncbi request reprint Likelihood-enhanced fast rotation functions
    Laurent C Storoni
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 60:432-8. 2004
    ..The likelihood-enhanced rotation targets have been implemented in the program Phaser...
  16. ncbi request reprint Structure of a serpin-protease complex shows inhibition by deformation
    J A Huntington
    Department of Haematology, University of Cambridge, Wellcome Trust Centre for Molecular Mechanisms in Disease, Cambridge Institute for Medical Research, UK
    Nature 407:923-6. 2000
    ..It is this ability of the conformational mechanism to crush as well as inhibit proteases that provides the serpins with their selective advantage...
  17. ncbi request reprint Likelihood-enhanced fast translation functions
    Airlie J McCoy
    Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 61:458-64. 2005
    ..These likelihood-enhanced translation targets for molecular-replacement searches have been implemented in the program Phaser using the Computational Crystallography Toolbox (cctbx)...
  18. ncbi request reprint Solution structure of the Kaposi's sarcoma-associated herpesvirus K3 N-terminal domain reveals a Novel E2-binding C4HC3-type RING domain
    Roger B Dodd
    Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Addenbrooke s Hospital, Hills Road, Cambridge CB2 2XY, UK
    J Biol Chem 279:53840-7. 2004
    ..Interaction with UbcH13 suggests a possible role for K3 in catalyzing Lys(63)-linked ubiquitination...
  19. ncbi request reprint Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing
    Navraj S Pannu
    Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 59:1801-8. 2003
    ..Test cases presented show that the newly derived multiple isomorphous replacement likelihood functions perform satisfactorily compared with currently used programs...
  20. ncbi request reprint Simple algorithm for a maximum-likelihood SAD function
    Airlie J McCoy
    University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, England
    Acta Crystallogr D Biol Crystallogr 60:1220-8. 2004
    ..Here, an alternative derivation of the P(SAD) function is described that leads to simplified algorithmic requirements and that allows an intuitive understanding of the expression...
  21. pmc High-resolution structure prediction and the crystallographic phase problem
    Bin Qian
    University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Box 357350, Seattle 98195, USA
    Nature 450:259-64. 2007
    ....
  22. ncbi request reprint Domain definition and target classification for CASP7
    Neil D Clarke
    Genome Institute of Singapore, 138627 Singapore
    Proteins 69:10-8. 2007
    ..A total of 28 target domains from the template-based modeling category were also assessed in the high accuracy category and four overlapped with the free modeling category...
  23. ncbi request reprint Swiveling domain mechanism in pyruvate phosphate dikinase
    Kap Lim
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
    Biochemistry 46:14845-53. 2007
    ..The trajectory of the His domain avoids major clashes with the partner domains while preserving the association of the two linker segments...
  24. ncbi request reprint Liberating crystallographers
    Randy J Read
    Structure 13:1236-7. 2005
    ..In this issue of Structure, DePristo et al. describe a new program, RAPPER, that should automate some of the most time-consuming tasks associated with rebuilding, refining, and completing protein crystal structures at moderate resolutions...
  25. ncbi request reprint Crystal structure of rab11 in complex with rab11 family interacting protein 2
    William N Jagoe
    School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
    Structure 14:1273-83. 2006
    ..The complex reveals the structural basis for Rab11 recognition by FIPs and suggests the molecular mechanisms underlying endocytic recycling pathways...
  26. ncbi request reprint PHENIX: building new software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 4 230, Berkeley, CA 94720, USA
    Acta Crystallogr D Biol Crystallogr 58:1948-54. 2002
    ..This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer...
  27. ncbi request reprint Recent developments in the PHENIX software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Synchrotron Radiat 11:53-5. 2004
    ..Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described...
  28. ncbi request reprint Automated server predictions in CASP7
    James N D Battey
    Biozentrum, University of Basel, Basel, Switzerland
    Proteins 69:68-82. 2007
    ..This article summarizes the contribution of automated structure prediction servers in the CASP7 experiment, with emphasis on 3D structure prediction, as well as information on their prediction scope and public availability...
  29. doi request reprint Automated structure solution with the PHENIX suite
    Peter H Zwart
    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Methods Mol Biol 426:419-35. 2008
    ..The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI...
  30. pmc Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 64:515-24. 2008
    ..The procedure is demonstrated with a molecular-replacement structure and with an experimentally phased structure and a variation on the method is demonstrated by removing model bias from a structure from the Protein Data Bank...
  31. pmc Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 64:61-9. 2008
    ..1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution...
  32. ncbi request reprint The application of multivariate statistical techniques improves single-wavelength anomalous diffraction phasing
    Navraj S Pannu
    Biophysical Structural Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
    Acta Crystallogr D Biol Crystallogr 60:22-7. 2004
    ....