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Publications

  1. 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, In press.
  2. Roche, D. B., Buenavista, M. T., & McGuffin, L. J. (2012) FunFOLDQA: A Quality Assessment Tool for Protein-Ligand Binding Site Residue Predictions. PLoS ONE, In press.
  3. 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.
    4. PubMed
  4. 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.
  5. 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.
    6. PubMed
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. McGuffin, L. J. (2010) Model Quality Prediction. In Protein Structure Prediction: Methods and Algorithms, Wiley, 323-342.
  12. 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
  13. 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.
  14. McGuffin, L. J. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24, 1789-1804. PubMed
  15. McGuffin, L. J. (2008) Protein fold recognition and threading, In Computational Structural Biology, World Scientific, 37-60.
  16. McGuffin, L. J. (2008) The ModFOLD Server for the Quality Assessment of Protein Structural Models. Bioinformatics, 24, 586-587. PubMed
  17. McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition, BMC Bioinformatics, 8, 345. PubMed
  18. McGuffin, L. J. (2007) Aligning sequences to structures. Methods Mol Biol., 413, 61-90. PubMed
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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.
  24. 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
  25. 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
  26. 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
  27. 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
  28. McGuffin, L. J., Street, S., Sorensen, S. A. & Jones, D. T. (2004) The Genomic Threading Database. Bioinformatics, 20, 131-132. PubMed
  29. 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
  30. 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
  31. 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
  32. 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)
  33. 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
  34. 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
  35. 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) 
  36. 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) 
  37. McGuffin, L. J., Bryson, K. & Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405.  PubMed

     

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