Research Topics
Species | David T JonesSummaryAffiliation: University College London Country: UK Publications
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Detail Information
Publications
High throughput profile-profile based fold recognition for the entire human proteomeLiam 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...
Assembling novel protein folds from super-secondary structural fragmentsDavid 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...- Prediction of novel and analogous folds using fragment assembly and fold recognitionD 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... - Structural biology. Learning to speak the language of proteinsDavid T Jones
Department of Computer Science and Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, UK
Science 302:1347-8. 2003 - Prediction of disordered regions in proteins from position specific score matricesDavid 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... - Improving the accuracy of transmembrane protein topology prediction using evolutionary informationDavid 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... - Protein structure prediction servers at University College LondonKevin 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... - 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... - Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithmTimothy 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/... - Protein topology from predicted residue contactsWilliam 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.... - Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methodsStefano 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... - Transmembrane protein topology prediction using support vector machinesTimothy 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... - Inferring function using patterns of native disorder in proteinsAnna 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... - Improving sequence-based fold recognition by using 3D model quality assessmentChris S Pettitt
Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
Bioinformatics 21:3509-15. 2005..This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information. CONTACT: .. - Predicting metal-binding site residues in low-resolution structural modelsJaspreet 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... - The DISOPRED server for the prediction of protein disorderJonathan 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/.. - The genomic threading databaseLiam 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. AVAILABILITY: http://bioinf.cs.ucl.ac.uk/GTD.. - Improvement of the GenTHREADER method for genomic fold recognitionLiam 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... - The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organismsLiam 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... - Docking protein domains in contact spaceStefano 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... 
pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discriminationAnna Lobley
Department of Computer Science, University College London, UK
Bioinformatics 25:1761-7. 2009....- BioRAT: extracting biological information from full-length papersDavid P A Corney
Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
Bioinformatics 20:3206-13. 2004..Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers... - Computational resources for the prediction and analysis of native disorder in proteinsMelissa 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... - Predictions of hot spot residues at protein-protein interfaces using support vector machinesStefano 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... - Rapid protein domain assignment from amino acid sequence using predicted secondary structureRussell 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... - Improving classification in protein structure databases using text miningAntonis 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... - PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignmentsDavid 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... - An automatic method for assessing structural importance of amino acid positionsMichael 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... - Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure predictionChing 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... - A meta-analysis of microarray gene expression in mouse stem cells: redefining stemnessYvonne 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... - The transmembrane topology of Batten disease protein CLN3 determined by consensus computational prediction constrained by experimental dataTimothy 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... - Computer-assisted protein domain boundary prediction using the DomPred serverKevin 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... - Membrane protein structural bioinformaticsTimothy Nugent
Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK
J Struct Biol 179:327-37. 2012.... - Towards genome-scale structure prediction for transmembrane proteinsNaama 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... - Benchmarking secondary structure prediction for fold recognitionLiam J McGuffin
Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom
Proteins 52:166-75. 2003.... - Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression dataYvonne 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... - The MEMPACK alpha-helical transmembrane protein structure prediction serverTimothy Nugent
Department of Computer Science, University College London, London, UK
Bioinformatics 27:1438-9. 2011..AVAILABILITY: The server can be accessed as a new component of the PSIPRED portal by at http://bioinf.cs.ucl.ac.uk/psipred/... - Introduction. Bioinformatics: from molecules to systemsDavid 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 - Getting the most from PSI-BLASTDavid 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... - Protein function prediction by massive integration of evolutionary analyses and multiple data sourcesDomenico 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... - Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysisTimothy 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... - Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degenerationRuodan 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... - Public participation in soil surveys: lessons from a pilot study in EnglandJames Bone
Centre for Environmental Policy, Imperial College London, London, United Kingdom
Environ Sci Technol 46:3687-96. 2012.... - Detecting pore-lining regions in transmembrane protein sequencesTimothy 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... - The implications of alternative splicing in the ENCODE protein complementMichael 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.... - ISPIDER Central: an integrated database web-server for proteomicsJennifer 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... - Targeting novel folds for structural genomicsLiam J McGuffin
Institute of Cancer Genetics and Pharmacogenomics, Department of Biological Sciences, Brunel University, Uxbridge, Middlesex, United Kingdom
Proteins 48:44-52. 2002.... - Protein evolution with dependence among codons due to tertiary structureDouglas M Robinson
Bioinformatics Research Center, North Carolina State University, USA
Mol Biol Evol 20:1692-704. 2003....