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McGuffin Group Publications

  1. Elofsson A., Joo K., Keasar C., Lee J., Maghrabi A.H.A., Manavalan B., McGuffin L.J., Ménendez Hurtado D., Mirabello C., Pilstål R., Sidi T., Uziela K. & Wallner B. (2017) Methods for estimation of model accuracy in CASP12. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.25395. [Epub ahead of print] PubMed (All authors contibuted equally and the list is sorted alphabetically)
  2. McGuffin, L.J., Shuid, A.M., Kempster, R., Maghrabi, A.H.A., Nealon  J.O., Salehe, B.R., Atkins, J.D. & Roche, D.B. (2017) Accurate Template Based Modelling in CASP12 using the IntFOLD4-TS, ModFOLD6 and ReFOLD methods. Proteins: Structure, Function, and Bioinformatics. doi: 10.1002/prot.25360. [Epub ahead of print] PubMed
  3. Maghrabi, A.H.A. & McGuffin, L.J. (2017) ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins. Nucleic Acids Research, doi: 10.1093/nar/gkx332. [Epub ahead of print]. PubMed (Both authors contributed equally to this work as first authors)
  4. Shuid, A.M., Kempster, R. & McGuffin, L.J. (2017) ReFOLD: a server for the refinement of 3D models of proteins guided by accurate quality estimates. Nucleic Acids Research, doi: 10.1093/nar/gkx249. [Epub ahead of print]. PubMed (All authors contributed equally to this work as first authors)
  5. Salehe, B.R., Jones C.I., Di Fatta, G. & McGuffin, L.J. (2017) RAPIDSNPS: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses. PLOS ONE, 12, e0175957. PubMed
  6. Uçarlı, C, McGuffin, L.J., Çaputlu, S. Aravena, A. & Gürel, F. (2016) Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses, Nature Sci. Rep., 6, 20966. PubMed
  7. Roche, D.B. & McGuffin, L.J. (2016) In silico identification and characterization of protein-ligand binding sites. In: Computational design of ligand binding proteins, Methods in Molecular Biology, 1414, 1-21. PubMed
  8. Roche, D.B. & McGuffin, L.J. (2016) Toolbox for protein structure prediction. In: Yeast Cytokinesis, Methods in Molecular Biology, 1369, 363-77. PubMed
  9. Roche, D.B., Brackenridge, D.A. & McGuffin, L.J. (2015) Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. Int. J. Mol. Sci., 16, 29829-29842. PubMed
  10. Atkins, J. D., Boateng, S. Y., Sorensen, T. & McGuffin, L. J. (2015) Disorder prediction methods, their applicability to different protein targets and their usefulness for guiding experimental studies. Int. J. Mol. Sci., 16, 19040-19054. PubMed
  11. McGuffin, L.J., Atkins, J., Salehe, B.R., Shuid, A.N. & Roche, D.B. (2015) IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences. Nucleic Acids Research, 43, W169-73. PubMed
  12. Taylor, T.B., Mulley, G., Dills, A.H., Alsohim, A.S., McGuffin, L. J., Studholme, D.J., Silby, M.W., Brockhurst, M.A., Johnson, L.J. and Jackson, R. W. (2015) Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science, 347, 1014-1017. PubMed
  13. Taylor, T.B., Mulley, G., McGuffin, L. J., Silby, M.W., Brockhurst, M.A., Arsenault, T., Studholme, D.J., Johnson, L.J. and Jackson, R. W. (2015) Evolutionary rewiring of bacterial regulatory networks. Microbial Cell. 2, 256-258.
  14. Wright, B., Watson, K.A., McGuffin, L.J., Lovegrove, J.A., Gibbins, J.M. (2015) GRID and Docking Analyses Reveal a Molecular Basis for Flavonoid Inhibition of Src-Family Kinase Activity. J. Nutr. Biochem., 26, 1156-1165. PubMed
  15. Monteagudo L.V., Ferrer, L.M., Catalan-Insa, E., Savva. D, McGuffin L. J., Tejedor, M.T. (2014) In silico identification and 3D modelling of the missense mutation in ADAMTS2 responsible for an ovine dermatosparaxis outbreak. Veterinary Dermatology, 26,49–e16. PubMed
  16. Tucci, V., Kleefstra, T., Hardy, A., Heise, I., Maggi, S., Willemsen, M. H., Hilton, H., Esapa, C., Simon, M., Buenavista, M. T., McGuffin, L. J. et al. (2014) Dominant β-­catenin mutations cause intellectual disability with recognizable syndromic features, J. Clin. Invest., 124, 1468-1482. PubMed
  17. Roche, D. B., Buenavista, M. T., McGuffin, L. J. (2014) Assessing the quality of modelled 3D protein structures using the ModFOLD server. Methods Mol. Biol., 1137, 83-103. PubMed
  18. Dunwell, T. L., McGuffin, L. J., Dunwell, J. M., & Pfeifer, G.P. (2013) The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome: possible explanations, Cell Cycle, 12, 0-8. PubMed
  19. Sugden, P. H., McGuffin, L. J. & Clerk, A. (2013) SOcK, MiSTs, MASK and STicKs - the germinal centre kinase III (GCKIII) kinases and their heterologous protein-protein interactions. Biochem J., 454, 13-30.
  20. PubMed
  21. Roche, D. B., Buenavista, M. T., McGuffin, L. J. (2013) The FunFOLD2 server for the prediction of protein-ligand interactions. Nucleic Acids Res., 41, W303-7. PubMed
  22. McGuffin, L. J. Buenavista, M. T., & Roche, D. B. (2013) The ModFOLD4 Server for the Quality Assessment of 3D Protein Models. Nucleic Acids Res., 41, W368-72. PubMed
  23. Pederson C., Ver Loren van Themaat, E., McGuffin, L.J., Abbott, J.C., Burgis, T.A., Barton, G., Bindschedler, L.V., Lu, X., Maekawa, T., Weßling, R., Cramer, R., Hans Thordal-Christensen, H., Panstruga, R. and Spanu, P.D. (2012) Structure and evolution of barley powdery mildew effector candidates. BMC Genomics, 13, 694. PubMed Highly Accessed
  24. Buenavista, M. T., Roche, D. B. & McGuffin, L. J. (2012) Improvement of 3D protein models using multiple templates guided by single-template model quality assessment. Bioinformatics, 28, 1851-1857. PubMed
  25. Roche, D. B., Buenavista, M. T. & McGuffin, L. J. (2012) FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions. PLOS ONE, 7, e38219. PubMed
  26. Fuller, S. J., McGuffin, L. J., Marshall, A. K., Giraldo, A., Pikkarainen, S., Clerk, A. & Sugden, P. H. (2012) A novel, non-canonical mechanism of regulation of mammalian Ste20-related kinase 3 (MST3). Biochem. J., 442, 595-610. PubMed
  27. Roche, D. B., Buenavista, M.T. & McGuffin, L. J. (2012) Predicting protein structures and structural annotation of proteomes. In Encyclopedia of Biophysics, Springer, In Press.
  28. McGuffin, L. J. & Roche, D. B. (2011) Automated tertiary structure prediction with accurate local model quality assessment using the IntFOLD-TS method. Proteins: Structure, Function, and Bioinformatics, 79 Suppl 10, 137-46.
  29. PubMed
  30. Roche, D. B., Tetchner, S. J. & McGuffin, L. J. (2011) FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. BMC Bioinformatics, 12, 160. PubMed
  31. Roche, D. B., Buenavista, M. T., Tetchner, S. J. & McGuffin, L. J. (2011) The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. Nucleic Acids Res., 39, W171-6. PubMed
  32. Bindschedler, L. V., McGuffin, L. J., Burgis, T. A., Spanu, P. D., Cramer, R. (2011) Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. Methods, 54, 432-441. (Joint first authorship with LVB). PubMed
  33. Roche, D. B., Tetchner, S. J. & McGuffin, L. J. (2010) The Binding Site Distance Test Score: A robust method for the assessment of predicted protein binding sites. Bioinformatics, 26, 2920-2921. PubMed
  34. McGuffin, L. J. & Roche, D. B. (2010) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics, 26, 182-188. PubMed
  35. McGuffin, L. J. (2010) Model Quality Prediction. In Protein Structure Prediction: Methods and Algorithms, Wiley, 323-342.
  36. McGuffin, L. J. (2009) Prediction of global and local model quality in CASP8 using the ModFOLD server. Proteins: Structure Function and Bioinformatics, 77, 185-190. PubMed
  37. McGuffin, L. J. (2009) Insertions and deletions, their molecular mechanisms and their impact on sequence alignments. In Sequence Alignments, University of California Press, 23-38.
  38. McGuffin, L. J. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24, 1789-1804.PubMed
  39. McGuffin, L. J. (2008) Protein fold recognition and threading, In Computational Structural Biology, World Scientific, 37-60.
  40. McGuffin, L. J. (2008) The ModFOLD Server for the Quality Assessment of Protein Structural Models. Bioinformatics, 24, 586-587.PubMed
  41. McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition, BMC Bioinformatics, 8, 345. PubMed
  42. McGuffin, L. J. (2007) Aligning sequences to structures. Methods Mol Biol., 413, 61-90. PubMed
  43. 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. PubMed
  44. Pettitt, C. S., McGuffin, L. J. & Jones, D. T. (2005) Improving sequenced based fold recognition by use of 3D model quality assessment. Bioinformatics, 21, 3509-3515. PubMed
  45. 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: Structure, Function and Bioinformatics, 61 Suppl 7, 143-51. PubMed
  46. McGuffin, L. J., Bryson, K, Marsden, R. L., Ward, J. J., Sodhi, J. S. & Jones, D. T. (2005) Protein Structure Prediction Servers at University College London. Nucleic Acids Res., 33, W36-8. (Joint first authorship with KB). PubMed
  47. Jones, D., Sodhi, J., Lise, S.,McGuffin, L., Bryson, K.(2005) Prediction of protein-protein and protein-ligand interactions from protein structures. FEBS JOURNAL 272 (s1), 397-398.
  48. 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. Nucleic Acids Res., 32, D196-D199. PubMed
  49. Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L. & Jones, D. T. (2004) Predicting metal binding sites in low resolution structural models. J. Mol. Biol., 342, 307-320. PubMed
  50. 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. PubMed
  51. 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. PubMed
  52. McGuffin, L. J., Street, S., Sorensen, S. A. & Jones, D. T. (2004) The Genomic Threading Database. Bioinformatics, 20, 131-132. PubMed
  53. Sodhi, J. S., McGuffin, L. J., Bryson, K., Ward, J. J., Wernisch, L. & Jones, D. T. (2004) Automatic prediction of functional site regions in low-resolution protein structures. Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (CSB2004), 702-703. Abstract PDF
  54. Jones, D. T. & McGuffin, L. J. (2003) Assembling Novel Protein Folds from Super-secondary Structural Fragments. Proteins: Structure, Function and Genetics, 53 (S6), 480-485. PubMed
  55. Ward, J. J., McGuffin, L. J., Buxton, B. F. & Jones, D. T. (2003) Secondary structure prediction using support vector machines. Bioinformatics, 19, 1650-1655. PubMed
  56. McGuffin, L. J. & Jones, D. T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881. PubMed (This paper was recognised by Thomson-ISI as a New Hot Paper)
  57. McGuffin, L. J. & Jones, D. T. (2003) Benchmarking protein secondary structure prediction for protein fold recognition. Proteins: Structure, Function and Genetics, 52, 166-175. PubMed
  58. Marsden, R., McGuffin, L. J. & Jones, D. T. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science, 11, 2814-2824.  PubMed
  59. McGuffin, L. J.& Jones, D.T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function and Genetics 48, 44-52.  PubMed
    (Supplementary information for this paper may be found at this link
  60. McGuffin, L. J., Bryson, K. & Jones, D. T. (2001) What are the baselines for protein fold recognition? Bioinformatics 17, 63-72.  PubMed
    (Supplementary information for this paper may be found at this link
  61. McGuffin, L. J., Bryson, K. & Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405.  PubMed

     

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