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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.
From structure to function: approaches and limitations.
Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA. Thornton JM, et al. Among authors: borkakoti n. Nat Struct Biol. 2000 Nov;7 Suppl:991-4. doi: 10.1038/80784. Nat Struct Biol. 2000. PMID: 11104008 Review.
Analysis of catalytic residues in enzyme active sites.
Bartlett GJ, Porter CT, Borkakoti N, Thornton JM. Bartlett GJ, et al. Among authors: borkakoti n. J Mol Biol. 2002 Nov 15;324(1):105-21. doi: 10.1016/s0022-2836(02)01036-7. J Mol Biol. 2002. PMID: 12421562
Finding enzyme cofactors in Protein Data Bank.
Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S. Mukhopadhyay A, et al. Among authors: borkakoti n. Bioinformatics. 2019 Sep 15;35(18):3510-3511. doi: 10.1093/bioinformatics/btz115. Bioinformatics. 2019. PMID: 30759194 Free PMC article.
Transform-MinER: transforming molecules in enzyme reactions.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Tyzack JD, et al. Among authors: borkakoti n. Bioinformatics. 2018 Oct 15;34(20):3597-3599. doi: 10.1093/bioinformatics/bty394. Bioinformatics. 2018. PMID: 29762650 Free PMC article.
Exploring Chemical Biosynthetic Design Space with Transform-MinER.
Tyzack JD, Ribeiro AJM, Borkakoti N, Thornton JM. Tyzack JD, et al. Among authors: borkakoti n. ACS Synth Biol. 2019 Nov 15;8(11):2494-2506. doi: 10.1021/acssynbio.9b00105. Epub 2019 Nov 5. ACS Synth Biol. 2019. PMID: 31647630 Free article.
41 results