Publications by David T. Jones (as of November 2022)

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Bibliometric data
Published papers 165
Total citations 52760
Average citations per paper 319
Average citations per year 1701
Max. citations per paper 7035
H-index 79

    Books

  1. Bioinformatics: Genes, Proteins and Computers

    2. Unpublished Papers and Technical Reports

  2. Improved CRC-64 algorithm for biological sequences
  3. On possible use of fold recognition models for molecular replacement
  4. Good Practice in (Pseudo) Random Number Generation for Bioinformatics Applications

    5. Published Research Papers

  5. Jones DT & Thornton JM (2022) The impact of AlphaFold2 one year on. Nat Methods, 19(1):15-20. doi: 10.1038/s41592-021-01365-3.
  6. Kandathil SM, Greener JG, Lau AM, Jones DT (2022) Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterised proteins. PNAS, 119(4):e2113348119. doi: 10.1073/pnas.2113348119.
  7. Greener JG, Kandathil SM, Moffat L, Jones DT (2021) A guide to machine learning for biologists. Nat Rev Mol Cell Biol, 23(1):40-55. doi: 10.1038/s41580-021-00407-0.
  8. Moffat L & Jones DT (2021) Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. Bioinformatics, 37(21):3744-3751. doi: 10.1093/bioinformatics/btab491.
  9. Greener JG & Jones DT (2021) Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins. PLOS One, 16(9):e0256990. doi: 10.1371/journal.pone.0256990.
  10. Wan C & Jones DT (2020) Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks. Nature Machine Intelligence. doi: 10.1038/s42256-020-0222-1.
  11. Buchan DWA & Jones DT (2020) Learning a functional grammar of protein domains using natural language word embedding techniques. 88(4):616-624. doi: 10.1002/prot.25842.
  12. Senior AW, Evans R, Jumper J, ..., Jones DT, ..., Hassabis D (2020). Improved protein structure prediction using potentials from deep learning. Nature. 577(7792):706-710. doi: 10.1038/s41586-019-1923-7.
  13. Senior AW, Evans R, Jumper J, ..., Jones DT, ..., Hassabis D (2019). Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13). Proteins. 87(12):1141-1148. doi: 10.1002/prot.25834.
  14. Greener JG, Kandathil SM, Jones DT (2019). Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints. Nature Communications, 10(1):3977. doi: 10.1038/s41467-019-11994-0.
  15. Kandathil SM, Greener JG, Jones DT (2019). Recent developments in deep learning applied to protein structure prediction. Proteins, 87(12):1179-1189. doi: 10.1002/prot.25824.
  16. Jones DT (2019). Setting the standards for machine learning in biology. Nature Reviews Molecular Cell Biology. 20(11):659-660. doi: 10.1038/s41580-019-0176-5.
  17. Kandathil SM, Greener JG, Jones DT (2019). Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13. Proteins, 87(12):1092-1099. doi: 10.1002/prot.25779.
  18. Clark WT, Kasak L, Bakolitsa C, ..., Jones DT, ..., LeBowitz JH (2019) Assessment of predicted enzymatic activity of ?-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Human Mutation doi: 10.1002/humu.23875.
  19. Clark WT, Kasak L, Bakolitsa C, ..., Jones DT, ..., LeBowitz JH (2019) Assessment of predicted enzymatic activity of ?-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Human Mutation doi: 10.1002/humu.23875.
  20. Wan C, Cozzetto D, Fa R, Jones DT (2019). Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks. PLoS One. 14(7):e0209958. doi: 10.1371/journal.pone.0209958.
  21. Buchan DWA, Jones DT (2019). The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz297.
  22. Fa R, Cozzetto D, Wan C, Jones DT (2018). Predicting human protein function with multi-task deep neural networks. PLoS One. 2018 Jun 11;13(6):e0198216. doi: 10.1371/journal.pone.0198216. eCollection 2018.
  23. Greener, J.G. Moffat, L. Jones, D.T. (2018) Design of metalloproteins and novel protein folds using variational autoencoders. Sci Rep. 2018 Nov 1;8(1):16189. doi: 10.1038/s41598-018-34533-1.
  24. Jones, D.T. Kandathil, S.M. (2018) High precision in protein contact prediction using fully convolutional neural networks and minimal sequence feature. Bioinformatics. 2018 Oct 1;34(19):3308-3315. doi: 10.1093/bioinformatics/bty341.
  25. Wan, C., Lees, J.G., Minneci, F., Orengo, C.A., Jones, D.T. (2017) Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PLoS computational biology doi: 10.1371/journal.pcbi.1005791.
  26. Buchan, D.W., Jones, D.T. (2017) Improved protein contact predictions with the MetaPSICOV2 server in CASP12. Proteins: Structure, Function, and Bioinformatics doi: 10.1002/prot.25379.
  27. Daneshjou, R., Wan, Y., ... Jones, D.T., ... (2017) Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation doi: 10.1002/humu.23280.
  28. Chandonia, J.M., Adhikari, A., Carraro, M., Chhibber, A., Cutting, G.R., Fu, Y., Gasparini, A., Jones, D.T., ... (2017) 3Lessons from the CAGI?4 Hopkins clinical panel challenge. Human Mutation doi: 10.1002/humu.23225.
  29. Xu, Q., Tang, Q., Katsonis, P., Lichtarge, O., Jones, D., Bovo, S., Babbi, G., ... (2017) Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Human Mutation doi: 10.1002/humu.23222.
  30. Giollo, M., Jones, D.T., Carraro, M., Leonardi, E., Ferrari, C., Tosatto, S.C.E. (2017) Crohn Disease Risk PredictionœôòóBest Practices and Pitfalls with Exome Data. Human Mutation doi: 10.1002/humu.23177.
  31. Kosciolek, T., Buchan, D.W.A., Jones, D.T. (2017) Predictions of backbone dynamics in Intrinsically disordered proteins using de novo fragment-based protein structure predictions. Scientific Reports doi: 10.1038/s41598-017-07156-1.
  32. Buchan, D.W., Jones, D.T. (2017) EigenTHREADER: Analogous protein fold recognition by efficient contact map threading. Bioinformatics doi: 10.1093/bioinformatics/btx217.
  33. Cozzetto, D., Jones, D.T. (2017) Computational methods for annotation transfers from sequence. The Gene Ontology Handbook doi: 10.1007/978-1-4939-3743-1.
  34. Nugent, T., Jones, D., Hayat, S. (2017) Advances in Computational Methods for Transmembrane Protein Structure Prediction. Protein Structure to Function with Bioinformatics doi: 10.1007/978-94-024-1069-3.
  35. Jiang, Y. Oron, T.R., ... Bryson, K., Cozzetto, D., Minneci, F., Jones, D.T., ... (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology 17:184.
  36. Cozzetto, D., Minneci, F., Currant, H., Jones, D.T. (2016) FFPred 3: feature-based function prediction for all Gene Ontology domains. Scientific Reports 6:31865.
  37. Drew,E., Jones, D.T., Wallace, B.A. (2016) Protein Design for Decreased Disorder: SHERP as an Exemplar Protein. Biophysical Journal 3 (110), 555a.
  38. Jones, D.T., Cozzetto, D. (2015) DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics 31 (6), 857-863.
  39. Jones, D.T., Singh, T., Kosciolek, T., Tetchner, S. (2015) MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics 31 (7), 999-1006.
  40. Kosciolek,T., Jones,D.T. (2015) Accurate contact predictions using covariation techniques and machine learning. Proteins: Structure, Function, and Bioinformatics 84(Suppl 1):145œôòó151.
  41. Kosciolek, T. & Jones, D.T. (2014) De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts. PloS one 9 (3), e92197A.
  42. van der Lee, R., Buljan, M., Lang, B., Weatheritt, R.J., Daughdrill, G.W., Dunker, A.K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D.T., Kim, P.M., Kriwacki, R.W., Oldfield, C.J., Pappu, R.V., Tompa, P., Uversky, V.N., Wright, P.E., Babu, M.M. (2014) Classification of Intrinsically Disordered Regions and Proteins. Chemical Reviews 114 (13) : 6589-6631.
  43. Nugent, T.C.O., Cozzetto, D. & Jones, D.T. (2014) Evaluation of predictions in the CASP10 model refinement category. Proteins: Structure, Function, and Bioinformatics 82 (S2) : 98-111.
  44. Nugent, T.C.O. & Jones, D.T. (2014) Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC bioinformatics 14 : 276.
  45. Buchan, D.W.A., Minneci, F., Nugent, T.C.O., Bryson, K & Jones, D.T. (2013) Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Research 41 (W1): W340-W348.
  46. Minneci, F., Piovesan, D., Cozzetto, D. & Jones, D.T. (2013) FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences. PLoS ONE 8(5): e63754. doi:10.1371/journal.pone.0063754
  47. Radivojac, P., Clark, W.T., Oron, T., Schnoes, A.M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., Pandey, G., Yunes, J.M., Talwalkar, A.S., Repo, S., Souza, M.L., Piovesan, D., Casadio, R., Wang, Z. Cheng, J., Fang, H., Gough, J., Koskinen, P., Toronen, P., Nokso-Koivisto, J., Holm, L., Cozzetto, D., Buchan, D.W.A., Bryson, K., Jones, D.T. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods. doi:10.1038/nmeth.2340.
  48. Cozzetto, D., Buchan, D.W.A, Bryson, K., & Jones, D.T. (2013) Protein function prediction by massive integration of evolutionary analyses and multiple data sources. BMC Bioinformatics. 14 (Suppl. 3), S1.
  49. Lewis, T.E., Sillitoe, I., Andreeva, A., Blundell, T.L., Buchan, D.W.A., Chothia, C., Cuff, A., Dana, J.M., Filippis, I., Gough, J., Hunter, S., Jones, D.T., Kelley, L.A., Kleywegt, G.J., Minneci, F., Mitchell, A., Murzin, A.G., Ochoa-Montano, B., Rackham, O.J.L, Smith, J., Sternberg, M.J.E., Velankar, S., Yeats, Orengo, C.A. (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic. Acid. Res. 41, D499-D507.
  50. Nugent, T.C.O. & Jones, D.T. (2012) Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis. Proc Natl Acad Sci U S A. 109, E1540-E1547.
  51. Jones, D.T., Buchan, D.W., Cozzetto, D. & Pontil, M. (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics. 28, 184-190.
  52. Taylor, W.R., Jones, D.T. & Sadowski, M.I. (2012) Protein topology from predicted residue contacts. Protein Sci. 21, 299-305.
  53. Nugent, T & Jones, D.T. (2012) Membrane protein structural bioinformatics. J. Struct. Biol. 179, 327-337
  54. Lise, S., Buchan, D., Pontil, M. & Jones, D.T. (2011) Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS One. e16774.
  55. Nugent, T.C.O., Ward, S & Jones, D.T. (2011) The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics. 27, 1438-1439.
  56. Nan, R., Farabella, I., Schumacher, F.F., Miller, A., Gor, J., Martin. A.C., Jones, D.T., Lengyel, I. & Perkins, S.J. (2011) Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration. J. Mol. Biol. 408, 714-735.
  57. Cuff, A.L., Sillitoe, I., Lewis, T., Clegg, A.B., Rentzsch, R,, Furnham, N., Pellegrini-Calace, M., Jones, D., Thornton, J. & Orengo, C.A. (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucl. Acids Res. 39, D420-D426.
  58. Buchan, D.W., Ward, S.M., Lobley, A.E., Nugent, T.C., Bryson, K. & Jones, D.T. (2010) Protein annotation and modelling servers at University College London. Nucl. Acids Res. 38 Suppl, W563-W568.
  59. Nugent, T.C.O. & Jones, D.T. (2010) Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm. Plos Comput. Biol.l. Biol. 6, e1000714604.
  60. Pentony, M.M., Ward, J. & Jones, D.T. (2010) Computational resources for the prediction and analysis of native disorder in proteins. Methods Mol. Biol. 604, 369-393.
  61. Pentony, M. & Jones, D.T. (2010) Modularity of intrinsic disorder in the human proteome. Proteins. 78, 212-221.
  62. Lise, S., Archambeau, C., Pontil, M. & Jones, D.T. (2009) Prediction of hot spot residues at protein-protein interfaces by combining machine learning and enERGY-BASed methods. BMC Bioinformatics. 10, 365.
  63. Nugent, T.C.O. & Jones, D.T. (2009) Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 10, 159. Epub.
  64. Edwards, Y.J., Lobley, A., Pentony, M.M. & Jones, D.T. (2009) Insights into the regulation of intrinsically disordered proteins in the human proteome by analysing sequence and gene expression data. Genome Biol. 10, R50. Epub.
  65. Lobley, A., Sadowski, M.I. & Jones, D.T. (2009) pGenTHREADER and pDomTHREADER: New Methods For Improved Protein Fold Recognition and Superfamily Discrimination. Bioinformatics. 25, 1761-1767.
  66. Koussounadis, A., Redfern, O.C. & Jones, D.T. (2009) Improving classification in protein structure databases using text mining. BMC Bioinformatics. 10, 12.
  67. Sadowski, M.I. & Jones, D.T. (2009) The sequence-structure relationship and protein function prediction. Curr. Opin. Struct. Biol. Apr 28.
  68. Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack, R.L. Jr, Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek, S.R. Jr, Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D., Wilson, I.A. (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure, 17, 151-159.
  69. Sadowski, M.I. & Jones, D.T. (2009) An automatic method for assessing structural importance of amino acid positions. BMC Struct Biol. 9:10.
  70. Edwards, Y.J., Bryson, K. & Jones, D.T. (2008) A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PLoS ONE. 3, e2712.
  71. Lobley, A.E., Nugent, T.C.O., Orengo, C.A. & Jones, D.T. (2008) FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res. May 7.
  72. Siepen, J.A., Belhajjame, K., Selley, J.N., Embury, S.M., Paton, N.W., Goble, C.A., Oliver, S.G., Stevens, R., Zamboulis, L., Martin, N., Poulovassillis, A., Jones, P., Cote, R., Hermjakob, H., Pentony, M.M., Jones, D.T., Orengo, C.A., Hubbard, S.J. (2008) ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res. 2008 Apr 25.
  73. Nugent, T.C.O., Mole, S. & Jones, D.T. (2008) The transmembrane topology of Batten disease protein CLN3 determined by consensus computational prediction constrained by experimental data. FEBS Lett. 582, 1019-1024.
  74. Tan, C. & Jones, D.T. (2008) Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics. 9, 94.
  75. Lobley, A., Swindells, M.B., Orengo, C.A. & Jones, D.T. (2007) Inferring function using patterns of native disorder in proteins. PLoS Comput. Biol. 3:e162.
  76. Sadowski, M.I. & Jones, D.T. (2007) Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins. 69, 476-485.
  77. Bryson, K., Cozzetto, D. & Jones, D.T. (2007) Computer-assisted protein domain boundary prediction using the DomPred server. Curr Protein Pept Sci., 8, 181-188.
  78. Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J., Yeats, C., Olason, P.L., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., Lopez, G., Sadowski, M.I., Watson, J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Storling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher C, Ramirez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigo, R. , Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M, Tramontano, A. & Valencia, A. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A. 104, 5495-5500.
  79. Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23, 538-544.
  80. Ebbels, T. M., Buxton, B. F. & Jones, D. T. (2006) springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'. Bioinformatics, 22, e99-e107.
  81. Berman, H. M., Burley, S. K., Chiu, W., Sali, A., Adzhubei, A., Bourne, P.E., Bryant, S.H., Dunbrack, R.L. Jr, Fidelis, K., Frank, J., Godzik, A., Henrick, K., Joachimiak, A., Heymann, B., Jones, D., Markley, J. L., Moult, J., Montelione, G. T., Orengo, C., Rossmann, M. G., Rost, B., Saibil, H., Schwede, T., Standley, D. M. & Westbrook, J. D. (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure, 14, 1211-1217.
  82. Lise, S., Walker-Taylor, A. & Jones, D. T. (2006) Docking protein domains in contact space. BMC Bioinformatics, 7, 310.
  83. McGuffin, L. J., Smith R. T., Bryson, K., Sorensen, S. A. & Jones, D. T. (2006) High throughput profile-profile based fold recognition for the entire Human proteome. BMC Bioinformatics, 7, 288.
  84. Hurwitz, N., Pellegrini-Calace, M., Jones, D.T. (2006) Towards genome-scale structure prediction for transmembrane proteins. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:465-475.
  85. Jones D.T., Bryson K., Coleman A., McGuffin L.J., Sadowski M.I., Sodhi J.S., Ward J.J. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins. 61 Suppl 7:143-51.
  86. Corney, D. P. A., Byrne, E.L., Buxton, B. F. & Jones, D.T. (2005) "A Logical Framework for Template Creation and Information Extraction", Foundations of Semantic Oriented Data and Web Mining workshop, part of ICDM2005 (the Fifth IEEE International Conference on Data Mining).
  87. Pettitt, C.S., McGuffin, L.J. & Jones, D.T. (2005) Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 21(17):3509-3515.
  88. Bryson, K., McGuffin, L. J., Marsden, R. L., Ward, J. J., Sodhi, J. S. & Jones, D. T. (2005) Protein structure prediction servers at University College London. Nucl. Acids Res. 33(Web Server issue):W36-38.
  89. Lise, S. & Jones, D. T. (2005) Sequence patterns associated with disordered regions in proteins. Proteins. 58, 144-150.
  90. Corney, D. P., Buxton, B. F., Langdon, W. B. & Jones, D. T. (2004) BioRAT: extracting biological information from full-length papers. Bioinformatics. 20, 3206-3213.
  91. Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L. & Jones, D. T. (2004) Predicting metal-binding site residues in low-resolution structural models. J. Mol. Biol., 342, 307-320.
  92. Ward, J. J., McGuffin, L. J., Bryson K., Buxton, B. F. & Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20, 2138-2139.
  93. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645.
  94. McGuffin, L.J., Street, S., Bryson, K., Sorensen, S.A., Jones, D.T. (2004) The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucl. Acids Res. 32, D196-199.
  95. McGuffin, L.J., Street, S., Sorensen, S.A., Jones, D.T. (2004) The genomic threading database. Bioinformatics. 20, 131-132.
  96. Jones, D.T. (2003) Learning to speak the language of proteins. Science. 302, 1347-1348.
  97. Jones, D.T. & Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins. S6, 573-578.
  98. Jones, D.T. & McGuffin, L.J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins. S6, 480-485.
  99. Robinson, D.M., Jones, D.T., Kishino, H., Goldman, N. & Thorne, J.L. (2003) Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20, 1692-1704.
  100. Ward, J.J., McGuffin, L.J., Buxton, B.F. & Jones, D.T. (2003) Secondary structure prediction using support vector machines. Bioinformatics, 19, 1650-1655.
  101. Tress, M.L., Jones, D.T. & Valencia, A. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol. 18, 705-718.
  102. McGuffin, L.J. & Jones, D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
  103. McGuffin, L.J. & Jones, D.T. (2003) Benchmarking protein secondary structure prediction for protein fold recognition. Proteins: Structure, Function and Genetics, 52, 166-175.
  104. Pellegrini-Calace, M., Carotti, A. & Jones, D.T. (2003) Folding in lipid membranes(FILM): a novel method for the prediction of small membrane protein 3-D structures. Proteins: Structure, Function and Genetics. 50, 537-545.
  105. Marsden, R.L., McGuffin, L.J. & Jones, D.T. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science. 11, 2814-2824.
  106. McGuffin, L. J. & Jones, D.T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function and Genetics 48, 44-52.
  107. Jones, D.T. & Swindells M.B. (2002) Getting the most from PSI-BLAST. TRENDS BIOCHEM SCI. 27, 161-164.
  108. Bryson, K, Luck, M., Joy, M. & Jones, D.T. (2001) Agent interaction for bioinformatics data management. Appl. Artif. Intell. 15, 917-947.
  109. Jones, D.T. (2001) Protein structure prediction in genomics. Brief. Bioinformatics. 2, 111-125.
  110. Jones, D.T., Swindells, M.B. & Fagan, R. (2001) The role of protein structure prediction in drug discovery. Ann. Rep. Med. Chem. 36, 211-225.
  111. Jones, D.T. (2001) Predicting novel protein folds by using FRAGFOLD. PROTEINS. Suppl 5, 127-132.
  112. Jones, D.T. (2001) Evaluating the potential of using fold-recognition models for molecular replacement. ACTA CRYSTALLOGR D. 57, 1428-1434.
  113. Jones, D.T. (2001) Critically assessing the state-of-the-art in protein structure prediction. Pharmacogenomics J. 1, 126-134.
  114. McGuffin L.J., Bryson K, Jones, D.T. (2001) What are the baselines for fold recognition? Bioinformatics 17, 63-72.
  115. Bryson, K., Luck, M., Joy, M. & Jones, D.T. (2000) Applying agents to bioinformatics in GeneWeaver. Lect. Notes Artif. Intell. 1860, 60-71.
  116. Jones, D.T. & Hadley, C. (2000) Threading methods for protein structure prediction. (In) Bioinformatics: Sequence, structure and databanks. Higgins, D. & Taylor, W.R. Eds., pp1-13, Springer-Verlag, Heidelberg.
  117. Jones, D.T. (2000) Protein structure prediction in the postgenomic era. Curr. Opin. Struct. Biol. 10, 371-379.
  118. Jones, D.T. (2000) A practical guide to protein structure prediction. Methods Mol. Biol. 143, 131-154.
  119. McGuffin L.J., Bryson K., Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405.
  120. Fulop, V. & Jones, D.T. (1999) Beta propellers: structural rigidity and functional diversity. Curr. Opin. Struct. Biol. 9, 715-721.
  121. Jones, D.T. (1999) Bioinformatics and the Y2K problem. Bioinformatics. 15, 955-956.
  122. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202.
  123. Hadley, C. & Jones, D.T. (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure. 7, 1099-1112.
  124. Fischer, D., Barret, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D.T., Karplus, K.J., Kelley, L.A., MacCallum, R.M., Pawowski, K., Rost, B., Rychlewski, L., Sternberg, M. (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins. Suppl 3, 209-217.
  125. Jones, D.T., Tress, M., Bryson, K. & Hadley, C. (1999) Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins. S3, 104-111.
  126. Jones, D.T. (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
  127. Jones, D.T. (1998) THREADER : Protein Sequence Threading by Double Dynamic Programming. (in) Computational Methods in Molecular Biology. Steven Salzberg, David Searls, and Simon Kasif, Eds. Elsevier Science. Chapter 13.
  128. Swindells, M.B., Orengo, C.A., Jones, D.T., Hutchinson, E.G. & Thornton, J.M. (1998) Contemporary approaches to protein structure classification. Bioessays. 20, 884-891.
  129. Jones, D.T. & Taylor, W.R. (1998) Towards structural genomics for transmembrane proteins. Biochem. Soc. Trans. 26, 429-438.
  130. Orengo, C.A., Martin, A.M., Hutchinson, G., Jones, S., Jones, D.T., Michie, A.D., Swindells, M.B. & Thornton, J.M. (1998) Classifying a protein in the CATH database of domain structures. Acta Cryst. D. 54, 1155-1167.
  131. Lio, P., Goldman, N., Thorne, J.L. & Jones, D.T. (1998) PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics. 14, 726-733.
  132. Goldman, N., Thorne, J.L. & Jones, D.T. (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics. 149, 445-458.
  133. Jones, D.T. (1998) Do transmembrane protein superfolds exist? FEBS Lett. 423, 281-285.
  134. Jones, D.T. (1997) Progress in protein structure prediction. Curr. Opin. Struct. Biol. 7, 377-387.
  135. Jones, D.T. (1997) Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs. PROTEINS. Suppl. 1, 185-191.
  136. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. & Thornton. J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure. 5, 1093-1108.
  137. Jones, D.T. & Thornton, J.M. (1996) Potential-energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.
  138. Hubbard, T., Tramontano, A., Barton, G., Jones, D., Sippl, M., Valencia, A., Lesk, A., Moult, J., Rost, B., Sander, C., Schneider, R., Lahm, A., Leplae, R., Buta, C., Eisenstein, M., Fjellstrom, O., Floeckner, H., Grossmann, JG., Hansen, J., Citterich, MH., Joergensen, F.S., Marchler-Bauer, A., Osuna, J., Park, J., Reinhardt, A., dePouplana, LR., Rojo-Dominguez, A., Saudek, V., Sinclair, J., Sturrock, S., Venclovas, C., Vinals, C. (1996) Update on protein structure prediction: Results of the 1995 IRBM workshop. Folding & Design. 1, R55-R63.
  139. Jones, D.T., Orengo, C.A. & Thornton, J.M. (1996) Protein folds and their recognition from sequence. (In) Prediction of Protein Structure. Practical Approach Series. Sternberg, M.J.E. Ed. IRL Press. pp 173-206.
  140. Goldman, N., Thorne, J.L. & Jones, D.T. (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol. 263, 196-208.
  141. Thorne, J.L., Goldman, N. & Jones, D.T. (1996) Combining protein evolution and secondary structure. Molecular biology and evolution. 13, 666-673.
  142. Jones, D.T., Moody, C.M., Uppenbrink, J., Viles, J.H., Doyle, P.M., Harris, C.J., Pearl, L.H., Sadler, P.J. & Thornton, J.M. (1996) Towards meeting the Paracelsus challenge - the design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50-percent sequence identity to an all-beta protein. Proteins. 24, 502-513.
  143. Miller, R.T., Jones, D.T. & Thornton, J.M. (1996) Protein fold recognition by sequence threading - tools and assessment techniques. FASEB J. 10, 171-178.
  144. Jones, D.T. (1995) Theoretical approaches to designing novel sequences to fit a given fold. Curr. Opin. Biotech. 6, 452-459.
  145. Thornton, J.M., Jones, D.T., MacArthur, M.W., Orengo, C.A. & Swindells, M.B. (1995) Protein folds - towards understanding folding from inspection of native structures. Phil. Trans. Royal Soc. Series B. 348, 71-79.
  146. Taylor, W.R. & Jones, D.T. (1995) Modelling and predicting alpha-helical transmembrane structures. (In) Protein folds - A Distance-Based Approach. Bohr, H. & Brunak, S. Eds. CRC Press. pp283-293.
  147. Jones, D.T., Miller, R.T. & Thornton, J.M. (1995) Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins. 23, 387-397.
  148. Thornton, J.M., Orengo, C.M., Jones, D.T. & Taylor, W.R. (1994) Protein motifs and folding recognition. Biophysical Journal. 66, 241.
  149. Orengo, C.A., Jones, D.T. & Thornton, J.M. (1994) Protein domain superfolds and superfamilies. Nature. 372, 631-634.
  150. Jones, D.T. (1994) De novo protein design using pairwise potentials and a genetic algorithm. Protein Science. 3, 567-574.
  151. Taylor, W.R., Jones, D.T. & Green, N.M. (1994) A method for alpha-helical integral membrane protein fold prediction. Proteins. 18, 281-294.
  152. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33, 3038-3048.
  153. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1994) A mutation data matrix for transmembrane proteins. FEBS Letts. 339, 269-275. Supplementary Material
  154. Swindells, M.B., Orengo, C.A., Jones, D.T., Pearl, L.H. & Thornton, J.M. (1993) Recurrence of a binding motif. Nature. 362, 299.
  155. Orengo, C.A., Flores, T.P., Jones, D.T., Taylor, W.R. & Thornton, J.M. (1993) Recurring structural motifs in proteins with different functions. Current Biology 3, 131-139.
  156. Wilson, S.A., Wachira, S.J., Drew, R.E., Jones, D.T. & Pearl, L.H. (1993) EMBO J. 12, 3637-3642.
  157. Taylor, W.R. & Jones, D.T. (1993) Deriving an amino acid distance matrix. J. Theor. Biol. 164, 6583.
  158. Taylor, W.R., Jones, D.T. & Segal, A.W. (1993) A structural model for the nucleotide binding domains of the flavocytochrome b245 chain. Protein Science 2, 1675-1685.
  159. Jones, D.T. & Thornton, J.M. (1993) Protein fold recognition. J. Comput. Aided Mol. Des. 7:439-456.
  160. Thornton, J.M., MacArthur, M.W., McDonald, I.K., Jones, D.T., Mitchell, J.B.O., Nandi, C.L., Price, S.L. & Zvelebil, M.J.J.M. (1993) Protein structures and complexes what they reveal about the interactions that stabilize them. Phil. Trans. Royal Soc. Series A Physical Sciences and Engineering 345, 113-129.
  161. Jones, D.T. (1993) More protein talk. Nature. 361, 694.
  162. Jones, D.T., Orengo, C.A., Taylor, W.R., and Thornton, J.M. Progress towards Recognising Protein Folds from Amino Acid Sequences. Proceedings of Miami Bio/Technology Winter Symposium, p124.
  163. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) A new approach to protein fold recognition. Nature 358, 86-89.
  164. Jones, D.T. (1992) A brief review of protein sequence pattern matching. (In) Patterns in protein sequence and structure. Taylor, W.R. Ed., pp11-28, Springer-Verlag, Heidelberg.
  165. Jones, D.T., Taylor, W.R. & Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci. 8, 275-282.
  166. Thornton, J.M., Flores, T.P., Jones, D.T. & Swindells, M.B. (1991) Prediction of progress at last. Nature (News and Views). 354, 105-106.
  167. Jones, D.T. (1991) Identification of Protein Consensus Sequences - book review. Biotechnology and Applied Biochemistry. 14, 247.
  168. Taylor, W.R. & Jones, D.T. (1991) Templates, consensus patterns and motifs. Curr. Opin. Struct. Biol. 1, 327-333.
  169. Jones, D.T. (1991) The application of fractal clustering to efficient molecular ray-tracing on low-cost computers. J. Mol. Graphics. 9, 249-253.
d.jones@cs.ucl.ac.uk