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McGuffin Group Publications
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Adiyaman, R. & McGuffin, L.J. (2019) Methods for the Refinement of Protein Structure 3D Models. Int J Mol Sci. 20, 2301. DOI PubMed
- 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
- 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
- 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
- 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)
- 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
- 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
- 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)
- 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)
- 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
- 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
- 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
- Roche, D.B. & McGuffin, L.J. (2016) Toolbox for protein structure prediction. In: Yeast Cytokinesis, Methods in Molecular Biology, 1369, 363-77. PubMed
- 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
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- 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.
PubMed
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 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.
PubMed
- 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
- 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
- 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
- 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
- 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
- McGuffin, L. J. (2010) Model Quality Prediction. In Protein Structure Prediction: Methods and Algorithms, Wiley, 323-342.
- 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
- 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.
- McGuffin, L. J. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24, 1789-1804.PubMed
- McGuffin, L. J. (2008) Protein fold recognition and threading, In Computational Structural Biology, World Scientific, 37-60.
- McGuffin, L. J. (2008) The ModFOLD Server for the Quality Assessment of Protein Structural Models. Bioinformatics, 24, 586-587.PubMed
- McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition, BMC Bioinformatics, 8, 345. PubMed
- McGuffin, L. J. (2007) Aligning sequences to structures. Methods Mol Biol., 413, 61-90. PubMed
- 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
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- McGuffin, L. J., Street, S.,
Sorensen, S. A. & Jones, D. T. (2004)
The Genomic Threading Database.
Bioinformatics, 20, 131-132.
PubMed
- 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
- 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
- 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
- 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)
- 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
- 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
- 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)
- 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)
- McGuffin, L. J., Bryson, K. &
Jones, D. T. (2000) The PSIPRED protein
structure prediction server.
Bioinformatics. 16, 404-405.
PubMed
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