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Uncovering new families and folds in the natural protein universe.
Nature. 2023 Oct;622(7983):646-653. doi: 10.1038/s41586-023-06622-3. Epub 2023 Sep 13.
Nature. 2023.
PMID: 37704037
Free PMC article.
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.
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.
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Geometricus represents protein structures as shape-mers derived from moment invariants.
Durairaj J, Akdel M, de Ridder D, van Dijk ADJ.
Durairaj J, et al. Among authors: akdel m.
Bioinformatics. 2020 Dec 30;36(Suppl_2):i718-i725. doi: 10.1093/bioinformatics/btaa839.
Bioinformatics. 2020.
PMID: 33381814
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Caretta - A multiple protein structure alignment and feature extraction suite.
Akdel M, Durairaj J, de Ridder D, van Dijk ADJ.
Akdel M, et al.
Comput Struct Biotechnol J. 2020 Apr 6;18:981-992. doi: 10.1016/j.csbj.2020.03.011. eCollection 2020.
Comput Struct Biotechnol J. 2020.
PMID: 32368333
Free PMC article.
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From sequence to function through structure: Deep learning for protein design.
Ferruz N, Heinzinger M, Akdel M, Goncearenco A, Naef L, Dallago C.
Ferruz N, et al. Among authors: akdel m.
Comput Struct Biotechnol J. 2022 Nov 19;21:238-250. doi: 10.1016/j.csbj.2022.11.014. eCollection 2023.
Comput Struct Biotechnol J. 2022.
PMID: 36544476
Free PMC article.
Review.
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Signal-based optical map alignment.
Akdel M, van de Geest H, Schijlen E, van Rijswijck IMH, Smid EJ, Sanchez-Perez G, de Ridder D.
Akdel M, et al.
PLoS One. 2021 Sep 30;16(9):e0253102. doi: 10.1371/journal.pone.0253102. eCollection 2021.
PLoS One. 2021.
PMID: 34591846
Free PMC article.
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PanTools: representation, storage and exploration of pan-genomic data.
Sheikhizadeh S, Schranz ME, Akdel M, de Ridder D, Smit S.
Sheikhizadeh S, et al. Among authors: akdel m.
Bioinformatics. 2016 Sep 1;32(17):i487-i493. doi: 10.1093/bioinformatics/btw455.
Bioinformatics. 2016.
PMID: 27587666
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