Research Topics
Genomes and Genes | R J ReadSummaryAffiliation: University of Cambridge Country: UK Publications
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Detail Information
Publications
Crystallography: crystallographic evidence for deviating C3b structureBert 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....- Intensity statistics in the presence of translational noncrystallographic symmetryRandy 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.... - A new generation of crystallographic validation tools for the protein data bankRandy 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... - Using SAD data in PhaserRandy 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... - Case-controlled structure validationRandy 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... 
Assessment of CASP7 predictions in the high accuracy template-based modeling categoryRandy 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...- Detecting outliers in non-redundant diffraction dataR 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... - New ways of looking at experimental phasingRandy 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... - Pushing the boundaries of molecular replacement with maximum likelihoodR 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... 
The S-to-R transition of corticosteroid-binding globulin and the mechanism of hormone releaseAiwu 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...- Experimental phasing: best practice and pitfallsAirlie 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.... - A redox switch in angiotensinogen modulates angiotensin releaseAiwu Zhou
Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
Nature 468:108-11. 2010.... - Structural mechanism for the carriage and release of thyroxine in the bloodAiwu 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... - Likelihood-enhanced fast rotation functionsLaurent 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... - Structure of a serpin-protease complex shows inhibition by deformationJ 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... - Likelihood-enhanced fast translation functionsAirlie 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)... - Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasingNavraj 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... - Solution structure of the Kaposi's sarcoma-associated herpesvirus K3 N-terminal domain reveals a Novel E2-binding C4HC3-type RING domainRoger 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... - Simple algorithm for a maximum-likelihood SAD functionAirlie 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... - High-resolution structure prediction and the crystallographic phase problemBin Qian
University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Box 357350, Seattle 98195, USA
Nature 450:259-64. 2007.... - Domain definition and target classification for CASP7Neil 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... - PHENIX: building new software for automated crystallographic structure determinationPaul 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... - Automated structure solution with the PHENIX suitePeter 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... - Iterative-build OMIT maps: map improvement by iterative model building and refinement without model biasThomas 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... - Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizardThomas 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... - Swiveling domain mechanism in pyruvate phosphate dikinaseKap 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... - Automated server predictions in CASP7James 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... - Crystal structure of rab11 in complex with rab11 family interacting protein 2William 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... - Liberating crystallographersRandy 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... - The application of multivariate statistical techniques improves single-wavelength anomalous diffraction phasingNavraj 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.... - Recent developments in the PHENIX software for automated crystallographic structure determinationPaul 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...