David T Jones

Summary

Affiliation: University College London
Country: UK

Publications

  1. pmc High throughput profile-profile based fold recognition for the entire human proteome
    Liam J McGuffin
    The Biocentre, University of Reading, Whiteknights, PO Box 221, Reading RG6 6AS, UK
    BMC Bioinformatics 7:288. 2006
  2. ncbi request reprint Assembling novel protein folds from super-secondary structural fragments
    David T Jones
    Department of Computer Science, Bioinformatics Unit, University College London, London, United Kingdom
    Proteins 53:480-5. 2003
  3. ncbi request reprint Prediction of novel and analogous folds using fragment assembly and fold recognition
    D T Jones
    Department of Computer Science, University College London, London, United Kingdom
    Proteins 61:143-51. 2005
  4. ncbi request reprint Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    David T Jones
    Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
    Bioinformatics 23:538-44. 2007
  5. ncbi request reprint Structural biology. Learning to speak the language of proteins
    David T Jones
    Department of Computer Science and Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, UK
    Science 302:1347-8. 2003
  6. ncbi request reprint Prediction of disordered regions in proteins from position specific score matrices
    David T Jones
    Department of Computer Science, Bioinformatics Unit, University College London, London, United Kingdom
    Proteins 53:573-8. 2003
  7. pmc Protein structure prediction servers at University College London
    Kevin Bryson
    Department of Computer Science, University College London Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 33:W36-8. 2005
  8. ncbi request reprint springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'
    Timothy M D Ebbels
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT
    Bioinformatics 22:e99-107. 2006
  9. pmc Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
    PLoS Comput Biol 6:e1000714. 2010
  10. pmc Scalable web services for the PSIPRED Protein Analysis Workbench
    Daniel W A Buchan
    Department of Computer Science, University College London, Gower Street, London, WC1E 6BT
    Nucleic Acids Res 41:W349-57. 2013

Detail Information

Publications52

  1. pmc High throughput profile-profile based fold recognition for the entire human proteome
    Liam J McGuffin
    The Biocentre, University of Reading, Whiteknights, PO Box 221, Reading RG6 6AS, UK
    BMC Bioinformatics 7:288. 2006
    ..We use the most recent profile-profile version of our mGenTHREADER software in order to annotate the latest version of the Human proteome against the latest sequence and structure databases in as short a time as possible...
  2. ncbi request reprint Assembling novel protein folds from super-secondary structural fragments
    David T Jones
    Department of Computer Science, Bioinformatics Unit, University College London, London, United Kingdom
    Proteins 53:480-5. 2003
    ..Although clear progress has been made in improving FRAGFOLD since CASP4, the ranking of final models still seems to be the main problem that needs to be addressed before the next CASP experiment...
  3. ncbi request reprint Prediction of novel and analogous folds using fragment assembly and fold recognition
    D T Jones
    Department of Computer Science, University College London, London, United Kingdom
    Proteins 61:143-51. 2005
    ..Disorder prediction was carried out using a new SVM-based version of DISOPRED. Attempts were also made at domain docking and "microdomain" folding in order to build complete chain models for some targets...
  4. ncbi request reprint Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    David T Jones
    Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
    Bioinformatics 23:538-44. 2007
    ..In order to improve transmembrane topology prediction, we evaluate the combined use of both integrated signal peptide prediction and evolutionary information in a single algorithm...
  5. ncbi request reprint Structural biology. Learning to speak the language of proteins
    David T Jones
    Department of Computer Science and Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, UK
    Science 302:1347-8. 2003
  6. ncbi request reprint Prediction of disordered regions in proteins from position specific score matrices
    David T Jones
    Department of Computer Science, Bioinformatics Unit, University College London, London, United Kingdom
    Proteins 53:573-8. 2003
    ..The overall Matthews' correlation coefficient for the submitted predictions is 0.34, which gives a more realistic impression of the overall accuracy of the method, though still indicates significant predictive power...
  7. pmc Protein structure prediction servers at University College London
    Kevin Bryson
    Department of Computer Science, University College London Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 33:W36-8. 2005
    ..More recent servers include DISOPRED for the prediction of protein dynamic disorder and DomPred for domain boundary prediction. These servers are available from our software home page at http://bioinf.cs.ucl.ac.uk/software.html...
  8. ncbi request reprint springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'
    Timothy M D Ebbels
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT
    Bioinformatics 22:e99-107. 2006
    ..Overall, springScape shows promise as a tool for the interpretation of microarray data in the context of relevant bioinformatic information...
  9. pmc Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
    PLoS Comput Biol 6:e1000714. 2010
    ..This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/...
  10. pmc Scalable web services for the PSIPRED Protein Analysis Workbench
    Daniel W A Buchan
    Department of Computer Science, University College London, Gower Street, London, WC1E 6BT
    Nucleic Acids Res 41:W349-57. 2013
    ..All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/. ..
  11. pmc Protein topology from predicted residue contacts
    William R Taylor
    Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
    Protein Sci 21:299-305. 2012
    ....
  12. pmc Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
    Stefano Lise
    Department of Computer Science, University College London, UK
    BMC Bioinformatics 10:365. 2009
    ..Such methods would also add to our understanding of the determinants of affinity and specificity in protein-protein recognition...
  13. pmc Inferring function using patterns of native disorder in proteins
    Anna Lobley
    Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom
    PLoS Comput Biol 3:e162. 2007
    ..The GO category classifiers generated can be used to provide more reliable predictions and further insights into the behaviour of orphan and unannotated proteins...
  14. ncbi request reprint Improving sequence-based fold recognition by using 3D model quality assessment
    Chris S Pettitt
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    Bioinformatics 21:3509-15. 2005
    ..We systematically test and evaluate whether the MQAP methods can successfully detect native-like models...
  15. ncbi request reprint Predicting metal-binding site residues in low-resolution structural models
    Jaspreet Singh Sodhi
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, WC1E 6BT, UK
    J Mol Biol 342:307-20. 2004
    ..High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site...
  16. pmc Transmembrane protein topology prediction using support vector machines
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    BMC Bioinformatics 10:159. 2009
    ..In the absence of structural data, sequence-based prediction methods allow TM protein topology to be investigated...
  17. ncbi request reprint Improvement of the GenTHREADER method for genomic fold recognition
    Liam J McGuffin
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, UK
    Bioinformatics 19:874-81. 2003
    ..The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins...
  18. ncbi request reprint The genomic threading database
    Liam J McGuffin
    Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    Bioinformatics 20:131-2. 2004
    ..Annotations are carried out by using our modified GenTHREADER software and through implementing grid technology...
  19. pmc The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
    Liam J McGuffin
    Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 32:D196-9. 2004
    ..On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures...
  20. ncbi request reprint The DISOPRED server for the prediction of protein disorder
    Jonathan J Ward
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    Bioinformatics 20:2138-9. 2004
    ..AVAILABILITY: The server can be accessed by non-commercial users at http://bioinf.cs.ucl.ac.uk/disopred/..
  21. pmc Docking protein domains in contact space
    Stefano Lise
    Department of Biochemistry and Molecular Biology, University College London, UK
    BMC Bioinformatics 7:310. 2006
    ..The search is performed with a simulated annealing algorithm directly in contact space...
  22. doi request reprint pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
    Anna Lobley
    Department of Computer Science, University College London, UK
    Bioinformatics 25:1761-7. 2009
    ....
  23. doi request reprint Computational resources for the prediction and analysis of native disorder in proteins
    Melissa M Pentony
    Department of Computer Science, University College London, Gower Street, London, UK
    Methods Mol Biol 604:369-93. 2010
    ..We also discuss resources where the results of predictions have been collated, making them publicly available to the wider biological community...
  24. ncbi request reprint BioRAT: extracting biological information from full-length papers
    David P A Corney
    Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    Bioinformatics 20:3206-13. 2004
    ..BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE...
  25. pmc Protein function prediction by massive integration of evolutionary analyses and multiple data sources
    Domenico Cozzetto
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
    BMC Bioinformatics 14:S1. 2013
    ..We report on the methodology we used for this challenge and on the lessons we learnt...
  26. pmc Rapid protein domain assignment from amino acid sequence using predicted secondary structure
    Russell L Marsden
    Bioinformatics Unit, Department of Computer Science, University College London, UK
    Protein Sci 11:2814-24. 2002
    ..These results have been put into context in relation to the results obtained from the other prediction methods assessed...
  27. pmc Predictions of hot spot residues at protein-protein interfaces using support vector machines
    Stefano Lise
    Department of Computer Science, University College London, London, United Kingdom
    PLoS ONE 6:e16774. 2011
    ..An implementation of the described method is available as a web server at http://bioinf.cs.ucl.ac.uk/hspred. It is free to non-commercial users...
  28. pmc Improving classification in protein structure databases using text mining
    Antonis Koussounadis
    Bioinformatics Group, Department of Computer Science, University College of London, London, WC1E 6BT, UK
    BMC Bioinformatics 10:129. 2009
    ..The method is based on the assumption that textual similarity between sets of documents relating to proteins reflects biological function similarities and can be exploited to make classification decisions...
  29. doi request reprint PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    David T Jones
    Department of Computer Science, Bioinformatics Group, Centre for Computational Statistics and Machine Learning, University College London, Malet Place, London WC1E 6BT, UK
    Bioinformatics 28:184-90. 2012
    ..Our method builds on work which had previously demonstrated corrections for phylogenetic and entropic correlation noise and allows accurate discrimination of direct from indirectly coupled mutation correlations in the MSA...
  30. pmc Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction
    Ching Wai Tan
    Department of Computer Science, University College London, London, UK
    BMC Bioinformatics 9:94. 2008
    ..Various features are extracted from the training dataset of positive and negative examples and used as inputs to the neural networks...
  31. pmc An automatic method for assessing structural importance of amino acid positions
    Michael I Sadowski
    Computer Science Department, University College London, Gower St, London, WC1E 6BT, UK
    BMC Struct Biol 9:10. 2009
    ..In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose...
  32. pmc A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness
    Yvonne J K Edwards
    Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
    PLoS ONE 3:e2712. 2008
    ..We investigated the value of a novel meta-analysis of microarray gene expression in mouse SCs to aid the elucidation of regulatory mechanisms common to SCs and particular SC types...
  33. doi request reprint The transmembrane topology of Batten disease protein CLN3 determined by consensus computational prediction constrained by experimental data
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, United Kingdom
    FEBS Lett 582:1019-24. 2008
    ..Surprisingly, varied topological predictions were made using different subsets of orthologous sequences, highlighting the challenges still remaining for bioinformatics...
  34. ncbi request reprint Computer-assisted protein domain boundary prediction using the DomPred server
    Kevin Bryson
    Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
    Curr Protein Pept Sci 8:181-8. 2007
    ..The DomPred server is available from the URL:http://bioinf.cs.ucl.ac.uk/software.html...
  35. pmc Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
    Tony E Lewis
    Institute of Structural and Molecular Biology, UCL, 636 Darwin Building, Gower Street, London, WC1E 6BT, UK
    Nucleic Acids Res 41:D499-507. 2013
    ..This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs)...
  36. pmc Detecting pore-lining regions in transmembrane protein sequences
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    BMC Bioinformatics 13:169. 2012
    ..Computational methods that can identify structural features from sequence alone are therefore of high importance...
  37. doi request reprint Membrane protein structural bioinformatics
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    J Struct Biol 179:327-37. 2012
    ....
  38. pmc The MEMPACK alpha-helical transmembrane protein structure prediction server
    Timothy Nugent
    Department of Computer Science, University College London, London, UK
    Bioinformatics 27:1438-9. 2011
    ....
  39. pmc Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data
    Yvonne J K Edwards
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    Genome Biol 10:R50. 2009
    ..Here, we describe a study examining these features to gain insights into the regulation of disordered proteins...
  40. pmc Towards genome-scale structure prediction for transmembrane proteins
    Naama Hurwitz
    Bioinformatics Unit, Department of Computer Science, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
    Philos Trans R Soc Lond B Biol Sci 361:465-75. 2006
    ..Our eventual aim is to apply these methods in tandem so that useful three-dimensional models can be built for a large fraction of the transmembrane protein domains in whole proteomes...
  41. ncbi request reprint Benchmarking secondary structure prediction for fold recognition
    Liam J McGuffin
    Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom
    Proteins 52:166-75. 2003
    ....
  42. ncbi request reprint Getting the most from PSI-BLAST
    David T Jones
    Bioinformatics Unit, Dept Computer Science, University College London, Gower St, WC1E 6BT, London, UK
    Trends Biochem Sci 27:161-4. 2002
    ..This article explains some of the key steps in getting the most from PSI-Blast, one of the most popular and powerful homology search programs currently available...
  43. pmc Introduction. Bioinformatics: from molecules to systems
    David T Jones
    University College London Department of Computer Science, Bioinformatics Unit Gower Street, London WC1E 6BT, UK
    Philos Trans R Soc Lond B Biol Sci 361:389-91. 2006
  44. pmc Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
    Timothy Nugent
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, United Kingdom
    Proc Natl Acad Sci U S A 109:E1540-7. 2012
    ..75 and an rmsd of only 5.7 Å over all 514 residues. These results suggest that FILM3 could be applicable to a wide range of transmembrane proteins of as-yet-unknown 3D structure given sufficient homologous sequences...
  45. pmc Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration
    Ruodan Nan
    Department of Structural and Molecular Biology, Division of Biosciences, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
    J Mol Biol 408:714-35. 2011
    ..Given the high pathophysiological levels of bioavailable zinc present in subretinal deposits, we discuss how zinc binding to FH may contribute to deposit formation and inflammation associated with AMD...
  46. doi request reprint The contribution of intrinsic disorder prediction to the elucidation of protein function
    Domenico Cozzetto
    Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
    Curr Opin Struct Biol 23:467-72. 2013
    ..Recent developments towards identifying functional sites in disordered regions, and analysing how the occurrence of protein disorder in a gene can provide insight into its biochemical and cellular function are discussed...
  47. pmc FFPred 2.0: improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences
    Federico Minneci
    Bioinformatics Group, Department of Computer Science, University College London, London, United Kingdom
    PLoS ONE 8:e63754. 2013
    ..We illustrate all these points through the use of both precision-recall plots and of the COGIC scores, which we recently proposed as an alternative numerical evaluation measure of function prediction accuracy...
  48. doi request reprint Public participation in soil surveys: lessons from a pilot study in England
    James Bone
    Centre for Environmental Policy, Imperial College London, London, United Kingdom
    Environ Sci Technol 46:3687-96. 2012
    ....
  49. ncbi request reprint Targeting novel folds for structural genomics
    Liam J McGuffin
    Institute of Cancer Genetics and Pharmacogenomics, Department of Biological Sciences, Brunel University, Uxbridge, Middlesex, United Kingdom
    Proteins 48:44-52. 2002
    ....
  50. ncbi request reprint Protein evolution with dependence among codons due to tertiary structure
    Douglas M Robinson
    Bioinformatics Research Center, North Carolina State University, USA
    Mol Biol Evol 20:1692-704. 2003
    ....
  51. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...
  52. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....