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Using mechanism similarity to understand enzyme evolution.
Ribeiro AJM, Riziotis IG, Tyzack JD, Borkakoti N, Thornton JM. Ribeiro AJM, et al. Among authors: borkakoti n. Biophys Rev. 2022 Dec 3;14(6):1273-1280. doi: 10.1007/s12551-022-01022-9. eCollection 2022 Dec. Biophys Rev. 2022. PMID: 36659981 Free PMC article. Review.
Enzyme function and evolution through the lens of bioinformatics.
Ribeiro AJM, Riziotis IG, Borkakoti N, Thornton JM. Ribeiro AJM, et al. Among authors: borkakoti n. Biochem J. 2023 Nov 29;480(22):1845-1863. doi: 10.1042/BCJ20220405. Biochem J. 2023. PMID: 37991346 Free PMC article. Review.
A structural biology community assessment of AlphaFold2 applications.
Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P. Akdel M, et al. Among authors: borkakoti n. Nat Struct Mol Biol. 2022 Nov;29(11):1056-1067. doi: 10.1038/s41594-022-00849-w. Epub 2022 Nov 7. Nat Struct Mol Biol. 2022. PMID: 36344848 Free PMC article.
GRaSP: a graph-based residue neighborhood strategy to predict binding sites.
Santana CA, Silveira SA, Moraes JPA, Izidoro SC, de Melo-Minardi RC, Ribeiro AJM, Tyzack JD, Borkakoti N, Thornton JM. Santana CA, et al. Among authors: borkakoti n. Bioinformatics. 2020 Dec 30;36(Suppl_2):i726-i734. doi: 10.1093/bioinformatics/btaa805. Bioinformatics. 2020. PMID: 33381849
41 results