2022

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

Yin, X.-X., Hadjiloucas, S. ORCID: https://orcid.org/0000-0003-2380-6114, Zhang, Y. and Tian, Z. (2022) MRI radiogenomics for intelligent diagnosis of breast tumors and accurate prediction of neoadjuvant chemotherapy responses — a review. Computer methods and programs in biomedicine, 214. 106510. ISSN 1872-7565 doi: https://doi.org/10.1016/j.cmpb.2021.106510

2021

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

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

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

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

2020

Hadjiloucas, S. ORCID: https://orcid.org/0000-0003-2380-6114 (2020) Interaction of light with matter in optical fiber sensors: a biomedical engineering perspective. In: Del Villar, I. and Matias, I. R. (eds.) Optical fiber sensors: fundamentals for development of optimized devices. IEEE Press Series on Sensors. Wiley-IEEE Press. ISBN 9781119534761

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)

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

2019

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

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

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

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

2018

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

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

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

2017

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

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

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

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