Article

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

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

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

Book or Report Section

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

Thesis

Adiyaman, R. (2021) Improvement of MD-based protocols for the refinement of 3D protein models. PhD thesis, University of Reading. doi: https://doi.org/10.48683/1926.00104643