Article

Gerencer, M. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767 (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. ISSN 1664-3224 (In Press)

McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkad297

McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Aldowsari, F. M. F., Alharbi, S. M. A. and Adiyaman, R. (2022) ModFOLD8: accurate global and local quality estimates for 3D protein models. Nucleic Acids Research, 49 (W1). W425-W430. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkab321

Kryshtafovych, A. ORCID: https://orcid.org/0000-0001-5066-7178, Moult, J. ORCID: https://orcid.org/0000-0002-3012-2282, Billings, W. M., Della Corte, D. ORCID: https://orcid.org/0000-0002-8884-9724, Fidelis, K. ORCID: https://orcid.org/0000-0002-8061-412X, Kwon, S., Olechnovič, K. ORCID: https://orcid.org/0000-0003-4918-9505, Seok, C. ORCID: https://orcid.org/0000-0002-1419-9888, Venclovas, Č., Won, J., Adiyaman, R. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767 (2021) Modeling SARS‐CoV2 proteins in the CASP ‐commons experiment. Proteins: Structure, Function, and Bioinformatics. ISSN 0887-3585 doi: https://doi.org/10.1002/prot.26231

Adiyaman, R. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767 (2021) ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. Nucleic Acids Research, 49 (W1). W589-W596. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkab300

Sahli, K. A., Flora, G. D., Sasikumar, P., Maghrabi, A. H., Holbrook, L., AlOuda, S. K., Elgheznawy, A., Sage, T., Stainer, A. R., Adiyaman, R., AboHassan, M., Crescente, M., Kriek, N., Vaiyapuri, S., Bye, A. P., Unsworth, A. J., Jones, C. I., McGuffin, L. J. and Gibbins, J. M. (2021) Structural, functional and mechanistic insights uncover the fundamental role of orphan connexin-62 in platelets. Blood, 137 (6). pp. 830-843. ISSN 0006-4971 doi: https://doi.org/10.1182/blood.2019004575

Fuller, S. J., Edmunds, N. S., McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Hardyman, M. A., Cull, J. J., Alharbi, H. O., Meijles, D. N., Sugden, P. H. and Clerk, A. ORCID: https://orcid.org/0000-0002-5658-0708 (2021) MAP4K4 expression in cardiomyocytes: multiple isoforms, multiple phosphorylations and interactions with striatins. Biochemical Journal, 478 (11). pp. 2121-2143. ISSN 0264-6021 doi: https://doi.org/10.1042/BCJ20210003

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). ISSN 1478-811X doi: https://doi.org/10.1186/s12964-020-00554-5

Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., Davis, L., Dogan, T., Atalay, V., Rifaioglu, A. S., Dalkiran, A., Cetin-Atalay, R., Zhang, C., Hurto, R. L., Freddolino, P. L., Zhang, Y., Bhat, P., Supek, F., Fernández, J. M., Gemovic, B., Perovic, V. R., Davidović, R. S., Sumonja, N., Veljkovic, N., Asgari, E., Mofrad, M. R. K., Profiti, G., Savojardo, C., Martelli, P. L., Casadio, R., Boecker, F., Kahanda, I., Thurlby, N., McHardy, A. C., Renaux, A., Saidi, R., Gough, J., Freitas, A. A., Antczak, M., Fabris, F., Wass, M. N., Hou, J., Cheng, J., Hou, J., Wang, Z., Romero, A. E., Paccanaro, A., Yang, H., Goldberg, T., Zhao, C., Holm, L., Törönen, P., Medlar, A. J., Zosa, E., Borukhov, I., Novikov, I., Wilkins, A., Lichtarge, O., Chi, P.-H., Tseng, W.-C., Linial, M., Rose, P. W., Dessimoz, C., Vidulin, V., Dzeroski, S., Sillitoe, I., Das, S., Lees, J. G., Jones, D. T., Wan, C., Cozzetto, D., Fa, R., Torres, M., Vesztrocy, A. W., Rodriguez, J. M., Tress, M. L., Frasca, M., Notaro, M., Grossi, G., Petrini, A., Re, M., Valentini, G., Mesiti, M., Roche, D. B., Reeb, J., Ritchie, D. W., Aridhi, S., Alborzi, S. Z., Devignes, M.-D., Emily Koo, D. C., Bonneau, R., Gligorijević, V., Barot, M., Fang, H., Toppo, S., Lavezzo, E., Falda, M., Berselli, M., Tosatto, S. C. E., Carraro, M., Piovesan, D., Rehman, H. U., Mao, Q., Zhang, S., Vucetic, S., Black, G. S., Jo, D., Larsen, D. J., Omdahl, A. R., Sagers, L. W., Suh, E., Dayton, J. B., McGuffin, L., Brackenridge, D. A., Babbitt, P. C., Yunes, J. M., Fontana, P., Zhang, F., Zhu, S., You, R., Zhang, Z., Dai, S., Yao, S., Tian, W., Cao, R., Chandler, C., Amezola, M., Johnson, D., Chang, J.-M., Liao, W.-H., Liu, Y.-W., Pascarelli, S., Frank, Y., Hoehndorf, R., Kulmanov, M., Boudellioua, I., Politano, G., Di Carlo, S., Benso, A., Hakala, K., Ginter, F., Mehryary, F., Kaewphan, S., Björne, J., Moen, H., Tolvanen, M. E. E., Salakoski, T., Kihara, D., Jain, A., Šmuc, T., Altenhoff, A., Ben-Hur, A., Rost, B., Brenner, S. E., Orengo, C. A., Jeffery, C. J., Bosco, G., Hogan, D. A., Martin, M. J., O’Donovan, C., Mooney, S. D., Greene, C. S., Radivojac, P. and Friedberg, I. (2019) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20 (1). 244. ISSN 1474-760X doi: https://doi.org/10.1186/s13059-019-1835-8

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. and Wallner, B. (2019) Estimation of model accuracy in CASP13. Proteins: Structure, Function, and Bioinformatics. ISSN 0887-3585 doi: https://doi.org/10.1002/prot.25767

El Sarraf, N., Gurel, F., Tufan, F. and 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 (6). ISSN 1932-6203 doi: https://doi.org/10.1371/journal.pone.0218120

McGuffin, L. J., Adiyaman, R., Maghrabi, A. H. A., Shuid, A. N., Brackenridge, D. A., Nealon, J. O. and Philomina, L. S. (2019) IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Research. gkz322. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkz322

Adiyaman, R. and McGuffin, L. J. (2019) Methods for the refinement of protein structure 3D models. International Journal of Molecular Sciences, 20 (9). 2301. ISSN 1422-0067 doi: https://doi.org/10.3390/ijms20092301

Keasar, C., McGuffin, L. J., Wallner, B., Chopra, G., Adhikari, B., Bhattacharya, D., Blake, L., Bortot, L. O., Cao, R., Dhanasekaran, B. K., Dimas, I., Faccioli, R. A., Faraggi, E., Ganzynkowicz, R., Ghosh, S., Ghosh, S., Giełdoń, A., Golon, L., He, Y., Heo, L., Hou, J., Khan, M., Khatib, F., Khoury, G. A., Kieslich, C., Kim, D. E., Krupa, P., Lee, G. R., Li, H., Li, J., Lipska, A., Liwo, A., Maghrabi, A. H. A., Mirdita, M., Mirzaei, S., Mozolewska, M. A., Onel, M., Ovchinnikov, S., Shah, A., Shah, U., Sidi, T., Sieradzan, A. K., Ślusarz, M., Ślusarz, R., Smadbeck, J., Tamamis, P., Trieber, N., Wirecki, T., Yin, Y., Zhang, Y., Bacardit, J., Baranowski, M., Chapman, N., Cooper, S., Defelicibus, A., Flatten, J., Koepnick, B., Popović, Z., Zaborowski, B., Baker, D., Cheng, J., Czaplewski, C., Delbem, A. C. B., Floudas, C., Kloczkowski, A., Ołdziej, S., Levitt, M., Scheraga, H., Seok, C., Söding, J., Vishveshwara, S., Xu, D. and Crivelli, S. N. (2018) An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports, 8 (1). 9939. ISSN 2045-2322 doi: https://doi.org/10.1038/s41598-018-26812-8

McGuffin, L., Shuid, A. N., Kempster, R., Maghrabi, A. H.A., Nealon, J. O., Salehe, B. R., Atkins, J. D. and Roche, D. B. (2018) Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods. Proteins: Structure, Function, and Bioinformatics, 86. pp. 335-344. ISSN 0887-3585 doi: https://doi.org/10.1002/prot.25360

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. and Wallner, B. (2018) Methods for estimation of model accuracy in CASP12. Proteins: Structure, Function, and Bioinformatics, 86. pp. 361-373. ISSN 1097-0134 doi: https://doi.org/10.1002/prot.25395

Nealon, J. O., Philomina, L. S. and McGuffin, L. J. (2017) Predictive and experimental approaches for elucidating protein–protein interactions and quaternary structures. International Journal of Molecular Sciences, 18 (12). 2623. ISSN 1422-0067 doi: https://doi.org/10.3390/ijms18122623

Maghrabi, A. H. A. and McGuffin, L. J. (2017) ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models. Nucleic Acids Research, 45 (W1). W416-W421. ISSN 0305-1048 doi: https://doi.org/10.1093/nar/gkx332

Shuid, A. N., Kempster, R. and McGuffin, L. J. (2017) ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates. Nucleic Acids Research, 45 (W1). W422-W428. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkx249

Salehe, B. R., Jones, C. I., Di Fatta, G. and McGuffin, L. (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 (4). e0175957. ISSN 1932-6203 doi: https://doi.org/10.1371/journal.pone.0175957

Ucarlı, C., McGuffin, L., Caputlu, S., Aravena, A. and Gurel, F. (2016) Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses. Scientific Reports, 6. 20966. ISSN 2045-2322 doi: https://doi.org/10.1038/srep20966

Roche, D. B., Brackenridge, D. A. and McGuffin, L. J. (2015) Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods. International Journal of Molecular Sciences, 16 (12). pp. 29829-29842. ISSN 1422-0067 doi: https://doi.org/10.3390/ijms161226202

Wright, B., Watson, K. A., McGuffin, L. J., Lovegrove, J. and Gibbins, J. M. (2015) GRID and docking analyses reveal a molecular basis for flavonoid inhibition of src-family kinase activity. Journal of Nutritional Biochemistry, 26 (11). pp. 1156-1165. ISSN 0955-2863 doi: https://doi.org/10.1016/j.jnutbio.2015.05.004

Atkins, J. D., Boateng, S. Y., Sorensen, T. and McGuffin, L. J. (2015) Disorder prediction methods, their applicability to different protein targets and their usefulness for guiding experimental studies. International Journal of Molecular Sciences, 16 (8). pp. 19040-19054. ISSN 1422-0067 doi: https://doi.org/10.3390/ijms160819040

McGuffin, L. J., Atkins, J. D., Salehe, B. R., Shuid, A. N. and Roche, D. B. (2015) IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences. Nucleic Acids Research, 43 (W1). W169-W173. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkv236

Taylor, T., Mulley, G., McGuffin, L., Johnson, L., Brockhurst, M., Arseneault, T., Silby, M. and Jackson, R. (2015) Evolutionary rewiring of bacterial regulatory networks. Microbial Cell, 2 (7). pp. 256-258. ISSN 2311-2638 doi: https://doi.org/10.15698/mic2015.07.215

Taylor, T. B., Mulley, G., Dills, A. H., Alsohim, A. S., McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Studholme, D. J., Silby, M. W., Brockhurst, M. A., Johnson, L. J. ORCID: https://orcid.org/0000-0002-0006-1511 and Jackson, R. W. (2015) Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science, 347 (6225). pp. 1014-1017. ISSN 0036-8075 doi: https://doi.org/10.1126/science.1259145

Monteagudo, L. V., Ferrer, L. M., Catalan-Insa, E., Savva, D., McGuffin, L. and Tejedor, M. T. (2014) In silico identification and three-dimensional modelling of the missense mutation in ADAMTS2 in a sheep flock with dermatosparaxis. Veterinary Dermatology, 26 (1). 49-e16. ISSN 0959-4493 doi: https://doi.org/10.1111/vde.12178

Tucci, V., Kleefstra, T., Hardy, A., Heise, I., Maggi, S., Willemsen, M. H., Hilton, H., Esapa, C., Simon, M., Buenavista, M.-T., McGuffin, L., Vizor, L., Dodero, L., Tsaftaris, S., Romero, R., Nillesen, W. N., Vissers, L. E. L. M., Kempers, M. J., Vulto-van Silfhout, A. T., Iqbal, Z., Orlando, M., Maccione, A., Lassi, G., Farisello, P., Constestabile, A., Tinarelli, F., Nieus, T., Raimondi, A., Greco, B., Cantatore, D., Gasparini, L., Berdondini, L., Bifone, A., Gozzi, A., Wells, S. and Nolan, P. M. (2014) Dominant β-catenin mutations cause intellectual disability with recognizable syndromic features. The Journal of Clinical Investigation, 124 (4). pp. 1468-1482. ISSN 0021-9738 doi: https://doi.org/10.1172/JCI70372

Dunwell, T., McGuffin, L., Dunwell, J. and Pfeifer, G. (2013) The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome: Possible explanations. Cell Cycle, 12 (21). 3357 -3365. ISSN 1538-4101 doi: https://doi.org/10.4161/cc.26540

Sugden, P. H., McGuffin, L. J. and Clerk, A. (2013) SOcK, MiSTs, MASK and STicKs: the GCKIII (germinal centre kinase III) kinases and their heterologous protein–protein interactions. Biochemical Journal, 454 (1). pp. 13-30. ISSN 0264-6021 doi: https://doi.org/10.1042/BJ20130219

Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2013) The FunFOLD2 server for the prediction of protein-ligand interactions. Nucleic Acids Research, 41 (W1). W303-W307. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkt498

McGuffin, L. J., Buenavista, M. T. and Roche, D. B. (2013) The ModFOLD4 server for the quality assessment of 3D protein models. Nucleic Acids Research, 41 (W1). W368-W372. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkt294

Pedersen, C., van Themaat, E. V., McGuffin, L., Abbott, J. C., Burgis, T. A., Barton, G., Bindschedler, L. V., Lu, X., Maekawa, T., Weßling, R., Cramer, R., Thordal-Christensen, H., Panstruga, R. and Spanu, P. D. (2012) Structure and evolution of barley powdery mildew effector candidates. BMC Genomics, 13 (1). p. 694. ISSN 1471-2164 doi: https://doi.org/10.1186/1471-2164-13-694

Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2012) FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions. PLoS ONE, 7 (5). e38219. ISSN 1932-6203 doi: https://doi.org/10.1371/journal.pone.0038219

Buenavista, M. T., Roche, D. B. and McGuffin, L. J. (2012) Improvement of 3D protein models using multiple templates guided by single-template model quality assessment. Bioinformatics, 28 (14). pp. 1851-1857. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/bts292

Fuller, S. J., McGuffin, L. J., Marshall, A. K., Giraldo, A., Pikkarainen, S., Clerk, A. and Sugden, P. (2012) A novel, non-canonical mechanism of regulation of MST3 (mammalian Sterile20-related kinase 3). Biochemical Journal, 442 (3). pp. 595-610. ISSN 0264-6021 doi: https://doi.org/10.1042/BJ20112000

Bindschedler, L. V., McGuffin, L. J., Burgis, T. A., Spanu, P. D. and Cramer, R. (2011) Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. Methods, 54 (4). pp. 432-441. ISSN 1046-2023 doi: https://doi.org/10.1016/j.ymeth.2011.03.006

Roche, D. B., Buenavista, M. T., Tetchner, S. J. and 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 Research, 39 (Web Server). W171-W176. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkr184

McGuffin, L. J. and 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 (S10). pp. 137-146. ISSN 1097-0134 doi: https://doi.org/10.1002/prot.23120

Roche, D. B., Tetchner, S. J. and McGuffin, L. J. (2011) FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. BMC Bioinformatics, 12 (1). p. 160. ISSN 1471-2105 doi: https://doi.org/10.1186/1471-2105-12-160

Roche, D. B., Tetchner, S. J. and McGuffin, L. J. (2010) The binding site distance test score: a robust method for the assessment of predicted protein binding sites. Bioinformatics, 26 (22). pp. 2920-2921. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/btq543

McGuffin, L. J. and Roche, D. B. (2010) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics, 26 (2). pp. 182-188. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/btp629

McGuffin, L. J. (2009) Prediction of global and local model quality in CASP8 using the ModFOLD server. Proteins-Structure Function and Bioinformatics, 77. pp. 185-190. ISSN 0887-3585 doi: https://doi.org/10.1002/prot.22491

Marsden, R. L., McGuffin, L. J. and Jones, D. T. (2009) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science, 11 (12). pp. 2814-2824. ISSN 09618368 doi: https://doi.org/10.1110/ps.0209902

McGuffin, L. J. (2008) Aligning sequences to structures. Methods in Molecular Biology, 413. pp. 61-90. ISSN 1064-3745

McGuffin, L. J. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24 (16). pp. 1798-1804. ISSN 1367-4803 doi: https://doi.org/10.1093/bioinformatics/btn326

McGuffin, L. J. (2008) The ModFOLD server for the quality assessment of protein structural models. Bioinformatics, 24 (4). pp. 586-587. ISSN 1367-4803 doi: https://doi.org/10.1093/bioinformatics/btn014

McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition. Bmc Bioinformatics, 8. p. 15. ISSN 1471-2105 doi: https://doi.org/10.1186/1471-2105-8-345

McGuffin, L. J., Smith, R. T., Bryson, K., Sorensen, S. A. and Jones, D. T. (2006) High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics, 7 (1). 288. ISSN 1471-2105 doi: https://doi.org/10.1186/1471-2105-7-288

Jones, D. T., Bryson, K., Coleman, A., McGuffin, L. J., Sadowski, M. I., Sodhi, J. S. and Ward, J. J. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins: Structure, Function, and Bioinformatics, 61 (S7). pp. 143-151. ISSN 1097-0134 doi: https://doi.org/10.1002/prot.20731

Pettitt, C. S., McGuffin, L. J. and Jones, D. T. (2005) Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics, 21 (17). pp. 3509-3515. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/bti540

Bryson, K., McGuffin, L. J., Marsden, R. L., Ward, J. J., Sodhi, J. S. and Jones, D. T. (2005) Protein structure prediction servers at University College London. Nucleic Acids Research, 33 (S2). W36-W38. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gki410

Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F. and Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20 (13). pp. 2138-2139. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/bth195

McGuffin, L. J., Street, S., Sorensen, S.-A. and Jones, D. T. (2004) The Genomic Threading Database. Bioinformatics, 20 (1). pp. 131-132. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/btg387

McGuffin, L. J., Street, S. A. , Bryson, K. , Sørensen, S.‐A. and Jones, D. T. (2004) The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Research, 32 (S1). D196-D199. ISSN 1362-4962 doi: https://doi.org/10.1093/nar/gkh043

Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L. and Jones, D. T. (2004) Predicting metal-binding site residues in low-resolution structural models. Journal of Molecular Biology, 342 (1). pp. 307-320. ISSN 0022-2836 doi: https://doi.org/10.1016/j.jmb.2004.07.019

Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F. and Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the Three Kingdoms of Life. Journal of Molecular Biology, 337 (3). pp. 635-645. ISSN 0022-2836 doi: https://doi.org/10.1016/j.jmb.2004.02.002

Jones, D. T. and McGuffin, L. J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins: Structure, Function, and Genetics, 53 (S6). pp. 480-485. ISSN 0887-3585 doi: https://doi.org/10.1002/prot.10542

McGuffin, L. J. and Jones, D. T. (2003) Benchmarking secondary structure prediction for fold recognition. Proteins: Structure, Function, and Genetics, 52 (2). pp. 166-175. ISSN 0887-3585 doi: https://doi.org/10.1002/prot.10408

McGuffin, L. J. and Jones, D. T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19 (7). pp. 874-881. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/btg097

Ward, J. J., McGuffin, L. J., Buxton, B. F. and Jones, D. T. (2003) Secondary structure prediction with support vector machines. Bioinformatics, 19 (13). pp. 1650-1655. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/btg223

McGuffin, L. J. and Jones, D. T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function, and Bioinformatics, 48 (1). pp. 44-52. ISSN 1097-0134 doi: https://doi.org/10.1002/prot.10129

McGuffin, L. J., Bryson, K. and Jones, D. T. (2001) What are the baselines for protein fold recognition? Bioinformatics, 17 (1). pp. 63-72. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/17.1.63

McGuffin, L. J., Bryson, K. and Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16 (4). pp. 404-405. ISSN 1460-2059 doi: https://doi.org/10.1093/bioinformatics/16.4.404

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Maghrabi, A. H. A., Aldowsari, F. M. F. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Quality estimates for 3D protein models. In: Filipek, S. (ed.) Homology Modeling: Methods and Protocols. Methods in Molecular Biology, 2627. Springer Nature, New York, pp. 101-118. ISBN 9781071629734 doi: https://doi.org/10.1007/978-1-0716-2974-1_6

Adiyaman, R. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2023) Using local protein model quality estimates to guide a molecular dynamics-based refinement strategy. In: Filipek, S. (ed.) Homology Modeling: Methods and Protocols. Methods in Molecular Biology. Springer Nature, New York, pp. 119-140. ISBN 9781071629734 doi: https://doi.org/10.1007/978-1-0716-2974-1_7

Alharbi, S. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767 (2022) Machine learning methods for predicting protein contacts. In: Kurgan, L. (ed.) Machine Learning in Bioinformatics of Protein Sequences: Algorithms, Databases and Resources for Modern Protein Bioinformatics. World Scientific, pp. 155-181. ISBN 9789811258572 doi: https://doi.org/10.1142/12899 (In Press)

Brackenridge, D. A. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2021) Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods with a focus on FunFOLD3. In: Cacace, A. M., Hickey, C. M. and Bekes, M. (eds.) Targeted Protein Degradation: Methods and Protocols. Methods in Molecular Biology, 2365. Springer, pp. 43-58. ISBN 9781071616642 doi: https://doi.org/10.1007/978-1-0716-1665-9

Edmunds, N. S. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2021) Computational methods for the elucidation of protein structure and interactions. In: Owens, R. J. (ed.) Methods Molecular Biology: Structural Proteomics. Methods Molecular Biology, 2305. Springer Nature, pp. 23-52. ISBN 9781071614068 doi: https://doi.org/10.1007/978-1-0716-1406-8_2

Maghrabi, A. H. A. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 (2020) Estimating the quality of 3D protein models using the ModFOLD7 server. In: Daisuke, K. (ed.) Protein Structure Prediction. Methods in Molecular Biology, 2165. Springer, pp. 69-81. ISBN 978-1-0716-0708-4 doi: https://doi.org/10.1007/978-1-0716-0708-4_4 (Protein Structure Prediction)

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: https://doi.org/10.1007/978-3-642-35943-9_418-1

Roche, D. B. and McGuffin, L. J. (2016) Toolbox for protein structure prediction. In: Sanchez-Diaz, A. and Perez, P. (eds.) Yeast Cytokinesis. Methods in Molecular Biology, 1369. Springer, pp. 363-377. ISBN 9781493931453 doi: https://doi.org/10.1007/978-1-4939-3145-3_23

Roche, D. B. and 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. Springer, pp. 1-21. ISBN 9781493935673 doi: https://doi.org/10.1007/978-1-4939-3569-7_1

Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2014) Assessing the quality of modelled 3D protein structures using the ModFOLD server. In: Protein Structure Prediction. Methods in Molecular Biology, 1137. Springer, pp. 83-103. ISBN 9781493903658 doi: https://doi.org/10.1007/978-1-4939-0366-5_7

Roche, D. B., Buenavista, M. T. and McGuffin, L. (2012) Predicting protein structures and structural annotation of proteomes. In: Roberts, G. (ed.) Encylopedia of Biophysics. Springer-Verlag, Berlin Heidelberg. ISBN 9783642167119

McGuffin, L. J. (2010) Model quality prediction. In: Rangwala, H. and Karypis, G. (eds.) Introduction to protein structure prediction: methods and algorithms. Wiley, pp. 323-342. ISBN 9780470470596

McGuffin, L. J. (2009) Insertions and deletions, their molecular mechanisms and their impact on sequence alignments. In: Rosenberg, M. S. (ed.) Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press, pp. 23-38. ISBN 9780520256972

McGuffin, L.J. (2008) Protein fold recognition and threading. In: Computational Structural Biology. World Scientific Publishing Ltd, pp. 37-60. ISBN 9789812778772

Sodhi, J. S., McGuffin, L. J., Bryson, K., Ward, J. J., Wernisch, L. and Jones, D. T. (2004) Automatic prediction of functional site regions in low-resolution protein structures. In: Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004. IEEE, pp. 702-703. doi: https://doi.org/10.1109/CSB.2004.1332551