Number of items: 86.
Genc, A. G. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(2024)
Beyond AlphaFold2: the impact of AI for the further improvement of protein structure prediction.
In: Kloczkowski, A., Kurgan, L. and Faraggi, E. (eds.)
Prediction of Protein Secondary Structure.
Methods in molecular biology, 2867.
Springer Protocols, New York, NY, pp. 121-139.
ISBN 9781071641958
doi: https://doi.org/10.1007/978-1-0716-4196-5_7
Maharaj, A. V. ORCID: https://orcid.org/0000-0001-8051-3866, Ishida, M., Rybak, A., Elfeky, R., Andrews, A. ORCID: https://orcid.org/0000-0003-2390-657X, Joshi, A., Elmslie, F., Joensuu, A. ORCID: https://orcid.org/0000-0002-7547-7458, Kantojärvi, K., Jia, R. Y., Perry, J. R. B. ORCID: https://orcid.org/0000-0001-6483-3771, O’Toole, E. A. ORCID: https://orcid.org/0000-0002-4084-4836, McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Hwa, V. ORCID: https://orcid.org/0000-0003-0517-9049 and Storr, H. L. ORCID: https://orcid.org/0000-0002-9963-1931
(2024)
QSOX2 deficiency-induced short stature, gastrointestinal dysmotility and immune dysfunction.
Nature Communications, 15 (1).
8420.
ISSN 2041-1723
doi: https://doi.org/10.1038/s41467-024-52587-w
Edmunds, N. S., Genc, A. G. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(2024)
Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes.
Bioinformatics, 40 (8).
btae491.
ISSN 1460-2059
doi: https://doi.org/10.1093/bioinformatics/btae491
McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 and Alharbi, S. M. A.
(2024)
ModFOLD9: a web server for independent estimates of 3D protein model quality.
Journal of Molecular Biology.
168531.
ISSN 1089-8638
doi: https://doi.org/10.1016/j.jmb.2024.168531
Edmunds, N. S., Alharbi, S. M.A., Genc, A. G., Adiyaman, R. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(2023)
Estimation of model accuracy in CASP15 using the ModFOLDdock server.
Proteins: Structure, Function, and Bioinformatics, 91 (12).
pp. 1871-1878.
ISSN 1097-0134
doi: https://doi.org/10.1002/prot.26532
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, 51 (W1).
W274-W280.
ISSN 1362-4962
doi: https://doi.org/10.1093/nar/gkad297
Gerencer, M. and McGuffin, L. J. 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, 14.
ISSN 1664-3224
doi: https://doi.org/10.3389/fimmu.2023.1177691
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. M. A. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(2023)
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/10.1142/9789811258589_0006
Adiyaman, R., Edmunds, N. S., Genc, A. G., Alharbi, S. M. A. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767
(2023)
Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.
Bioinformatics Advances, 3 (1).
vbad078.
ISSN 2635-0041
doi: https://doi.org/10.1093/bioadv/vbad078
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, 89 (12).
pp. 1987-1996.
ISSN 0887-3585
doi: https://doi.org/10.1002/prot.26231
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
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. ORCID: https://orcid.org/0000-0002-6006-6517, Bye, A. P. ORCID: https://orcid.org/0000-0002-2061-2253, Unsworth, A. J., Jones, C. I. ORCID: https://orcid.org/0000-0001-7537-1509, McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 and Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352
(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
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
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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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
Roche, D. B., Buenavista, M. T. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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
Nealon, J. O., Philomina, L. S. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0001-7537-1509, Di Fatta, G. and McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767
(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
Roche, D. B. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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
Ucarlı, C., McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0002-9987-8539, McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Lovegrove, J. ORCID: https://orcid.org/0000-0001-7633-9455 and Gibbins, J. M. ORCID: https://orcid.org/0000-0002-0372-5352
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-0650-478X, McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767, Johnson, L. ORCID: https://orcid.org/0000-0002-0006-1511, 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. ORCID: https://orcid.org/0000-0003-0650-478X, 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. ORCID: https://orcid.org/0000-0003-4501-4767 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
Roche, D. B., Buenavista, M. T. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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
Tucci, V., Kleefstra, T., Hardy, A., Heise, I., Maggi, S., Willemsen, M. H., Hilton, H., Esapa, C., Simon, M., Buenavista, M.-T., McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, Dunwell, J. ORCID: https://orcid.org/0000-0003-2147-665X and Pfeifer, G.
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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. ORCID: https://orcid.org/0000-0003-4501-4767 and Clerk, A. ORCID: https://orcid.org/0000-0002-5658-0708
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, Abbott, J. C., Burgis, T. A., Barton, G., Bindschedler, L. V., Lu, X., Maekawa, T., Weßling, R., Cramer, R. ORCID: https://orcid.org/0000-0002-8037-2511, 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. ORCID: https://orcid.org/0000-0003-4501-4767
(2012)
Predicting protein structures and structural annotation of proteomes.
In: Roberts, G. (ed.)
Encylopedia of Biophysics.
Springer-Verlag, Berlin Heidelberg.
ISBN 9783642167119
Roche, D. B., Buenavista, M. T. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767, Marshall, A. K., Giraldo, A., Pikkarainen, S., Clerk, A. ORCID: https://orcid.org/0000-0002-5658-0708 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. ORCID: https://orcid.org/0000-0003-4501-4767, Burgis, T. A., Spanu, P. D. and Cramer, R. ORCID: https://orcid.org/0000-0002-8037-2511
(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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767
(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
McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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
Roche, D. B., Tetchner, S. J. and McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767
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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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767
(2008)
Aligning sequences to structures.
Methods in Molecular Biology, 413.
pp. 61-90.
ISSN 1064-3745
McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767
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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. ORCID: https://orcid.org/0000-0003-4501-4767
(2008)
Protein fold recognition and threading.
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World Scientific Publishing Ltd, pp. 37-60.
ISBN 9789812778772
McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767
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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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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
Sodhi, J. S., McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, Bryson, K., Ward, J. J., Wernisch, L. and Jones, D. T.
(2004)
Automatic prediction of functional site regions in low-resolution protein structures.
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Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.
IEEE, pp. 702-703.
doi: https://doi.org/10.1109/CSB.2004.1332551
Ward, J. J., McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767
(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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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. ORCID: https://orcid.org/0000-0003-4501-4767, 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
This list was generated on Sun Dec 22 14:02:26 2024 UTC.