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McGuffin Group Publications

  1. Genc, A. G. and McGuffin, L. J. (2025) Beyond AlphaFold2: The Impact of AI for the Further Improvement of Protein Structure Prediction. In: Kloczkowski, A., Kurgan, L., Faraggi, E. (eds) Prediction of Protein Secondary Structure. Methods in Molecular Biology, vol 2867. Humana, New York, NY. DOI PubMed
  2. Maharaj, A.V., Ishida, M., Rybak, A., Elfeky, R., Andrews, A., Joshi, A., Elmslie, F., Joensuu, A., Kantojärvi, K., Jia, R. Y., Perry, J. R. B., O’Toole, E. A., McGuffin, L. J., Hwa, V., & Storr, H. L. (2024) QSOX2 Deficiency-induced short stature, gastrointestinal dysmotility and immune dysfunction. Nature Communications, 15, 8420. DOI PubMed
  3. Edmunds, N. S., Genc, A. G. and McGuffin, L. J. (2024) Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking - a comparison with independent model quality assessment programs. Bioinformatics, 40, btae491. DOI PubMed
  4. McGuffin, L.J. and Alharbi, S. M. A. (2024) ModFOLD9: a web server for independent estimates of 3D protein model quality. Journal of Molecular Biology, 436, 168531. DOI PubMed
  5. Gerencer, M. and McGuffin, L. J. (2023) Are the integrin binding motifs within SARS CoV-2 spike protein and MHC class II alleles playing the key role in COVID-19? Frontiers in Immunology, 14, 1177691. DOI PubMed
  6. Adiyaman, R., Edmunds, N. S., Genc, A. G., Alharbi, S. M. A. and McGuffin, L. J. (2023) Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process. Bioinformatics Advances, vbad078. DOI PubMed
  7. Edmunds, N. S., Alharbi, S. M. A., Genc, A. G., Adiyaman, R. and McGuffin, L. J. (2023) Estimation of Model Accuracy in CASP15 Using the ModFOLDdock Server. Proteins, Epub ahead of print. DOI PubMed
  8. McGuffin, L. J., Edmunds N. S., Genc, A. G., Alharbi, S. M. A., Salehe, B. R. and Adiyaman, R. (2023) Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers. Nucleic Acids Research. gkad297. DOI PubMed
  9. Maghrabi, A. H. A. , Aldowsari, F. , McGuffin, L. J. (2023) Quality estimates for 3D protein models. In: Filipek, S., (eds.) Homology modeling: methods and protocols. Methods in Molecular Biology, 2627, 101-118. Springer Nature, New York. DOI PubMed
  10. Adiyaman, R. and McGuffin, L. J. (2023) Using local protein model quality estimates to guide a molecular dynamics-based refinement strategy. Methods in Molecular Biology, 2627, 119-140. Springer Nature, New York. DOI PubMed
  11. Alharbi, S. and McGuffin, L. J. (2022) Machine learning methods for predicting protein contacts. In: Kurgan, L., (eds.) Machine Learning in Bioinformatics of Protein Sequences: Algorithms, Databases and Resources for Modern Protein Bioinformatics. World Scientific pp. 155-181. DOI
  12. Kryshtafovych A., Moult, J., Billings, W.M., Della Corte, D., Fidelis, K., Kwon, S., Olechnovič, K., Seok, C., Venclovas, C., Won, J., and CASP-COVID participants with Adiyaman, R.,...McGuffin L. J. et al. (2021) Modeling SARS-CoV2 proteins in the CASP-commons experiment. Proteins, 89, 1987-1996. DOI PubMed
  13. Brackenridge, D. and McGuffin, L. J. (2021) Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods with a focus on FunFOLD3. In: Cacace, A., Hickey, C. and Bekes, M. (eds.) Targeted Protein Degradation: Methods and Protocols. Methods in Molecular Biology, 2365. Springer. DOI PubMed
  14. Fuller, S.J., Edmunds, N. S., McGuffin, L. J., Hardyman, M. A., Cull, J. A., Alharbi, H. O., Meijles, D., Sugden, P. H. & Clerk, A. (2021) MAP4K4 expression in cardiomyocytes: multiple isoforms and multiple phosphorylations and interactions with striatins. Biochem J., 478, 2121–2143. DOI PubMed
  15. McGuffin, L.J., Aldowsari, F., Alharbi, S. and Adiyaman, R. (2021) ModFOLD8: accurate global and local quality estimates for 3D protein models. Nucleic Acids Research, 49, W425–W430. DOI PubMed
  16. Adiyaman, R. & McGuffin, L.J. (2021) ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. Nucleic Acids Research, 49, W589–W596. DOI PubMed
  17. Edmunds, N. S. & McGuffin, L.J. (2021) Computational Methods for the Elucidation of Protein Structure and Interactions. Methods Mol. Biol., 2305, 23-52. DOI PubMed
  18. Sahli, K. A., Flora, G. D., Sasikumar, P., Maghrabi, A. H., Holbrook, L., AlOuda, S. K., Elgheznawy, A., Sage, T., Stainer, A., Adiyaman, R., AboHassan, M., Crescente, M., Kriek, N., Vaiyapuri, S., Bye, A., Unsworth, A., Jones, C., McGuffin, L. J. and Gibbins, J. (2021) Structural, functional and mechanistic insights uncover the fundamental role of orphan connexin 62 in platelets. Blood. 13, 830–843. DOI PubMed
  19. Maghrabi, A. H. A. and McGuffin, L. J. (2020) Estimating the quality of 3D protein models using the ModFOLD7 server. In: Protein Structure Prediction. Methods in Molecular Biology, 2165. Springer, pp. 69-81. DOI PubMed
  20. Tomkins, J.E., Ferrari, R., Vavouraki, N., Hardy, J., Lovering, R.C., Lewis, P.A., McGuffin, L.J. and Manzoni, C. (2020) PINOT: an intuitive resource for integrating protein-protein interactions. Cell Communication and Signaling. 18, 92. DOI PubMed
  21. Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J....McGuffin, L.J., Brackenridge, D. A....et al., (2019) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20, 244. DOI PubMed
  22. Cheng, J., Choe, M.H., Elofsson, A., Han, K.S., Hou, J., Maghrabi, A.H.A., McGuffin, L.J., Menéndez-Hurtado, D., Olechnovič, K., Schwede, T., Studer, G., Uziela, K., Venclovas, Č. & Wallner, B. (2019) Estimation of model accuracy in CASP13. Proteins: Structure, Function, and Bioinformatics. 87, 1361-1377. DOI PubMed
  23. El Sarraf N., Gurel F., Tufan F. & McGuffin, L.J. (2019) Characterisation of HvVIP1 and expression profile analysis of stress response regulators in barley under Agrobacterium and Fusarium infections. PLOS ONE. 14, e0218120. DOI PubMed
  24. Adiyaman, R. & McGuffin, L.J. (2019) Methods for the Refinement of Protein Structure 3D Models. Int J Mol Sci. 20, 2301. DOI PubMed
  25. McGuffin, L.J., Adiyaman, R., Maghrabi, A.H.A., Shuid, A.N., Brackenridge, D.A., Nealon, J.O. & Philomina, L.S. (2019) IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Research, 47, W408-W413. DOI PubMed
  26. Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2018) Protein structure prediction and structural annotation of proteomes. In: Encyclopedia of Biophysics. Springer. DOI
  27. Keasar C., McGuffin, L.J., Wallner, B et al. (2018) An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12, Nature Sci. Rep., 8, 9939. PubMed
  28. 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. (2018) Methods for estimation of model accuracy in CASP12. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1, 361-373, doi: 10.1002/prot.25395. PubMed (All authors contibuted equally and the list is sorted alphabetically)
  29. McGuffin, L.J., Shuid, A.N., Kempster, R., Maghrabi, A.H.A., Nealon  J.O., Salehe, B.R., Atkins, J.D. & Roche, D.B. (2018) Accurate Template Based Modelling in CASP12 using the IntFOLD4-TS, ModFOLD6 and ReFOLD methods. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1, 335-344, doi: 10.1002/prot.25360. PubMed
  30. Nealon J.O., Philomina L.S. & McGuffin L.J. (2017) Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. Int J Mol Sci. 18(12). 2623. doi: 10.3390/ijms18122623. PubMed
  31. 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, 45, W416-W421, doi: 10.1093/nar/gkx332. PubMed (Both authors contributed equally to this work as first authors)
  32. Shuid, A.N., 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, 45, W422-W428, doi: 10.1093/nar/gkx249. PubMed (All authors contributed equally to this work as first authors)
  33. 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
  34. 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
  35. 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
  36. Roche, D.B. & McGuffin, L.J. (2016) Toolbox for protein structure prediction. In: Yeast Cytokinesis, Methods in Molecular Biology, 1369, 363-77. PubMed
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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.
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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.
    48. PubMed
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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.
  55. 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.
    56. PubMed
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. McGuffin, L. J. (2010) Model Quality Prediction. In Protein Structure Prediction: Methods and Algorithms, Wiley, 323-342.
  62. 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
  63. 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.
  64. McGuffin, L. J. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24, 1789-1804.PubMed
  65. McGuffin, L. J. (2008) Protein fold recognition and threading, In Computational Structural Biology, World Scientific, 37-60.
  66. McGuffin, L. J. (2008) The ModFOLD Server for the Quality Assessment of Protein Structural Models. Bioinformatics, 24, 586-587.PubMed
  67. McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition, BMC Bioinformatics, 8, 345. PubMed
  68. McGuffin, L. J. (2007) Aligning sequences to structures. Methods Mol Biol., 413, 61-90. PubMed
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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.
  74. 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
  75. 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
  76. 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
  77. 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
  78. McGuffin, L. J., Street, S., Sorensen, S. A. & Jones, D. T. (2004) The Genomic Threading Database. Bioinformatics, 20, 131-132. PubMed
  79. 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
  80. 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
  81. 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
  82. 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)
  83. 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
  84. 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
  85. 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) 
  86. 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) 
  87. McGuffin, L. J., Bryson, K. & Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405.  PubMed

     

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