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Wybrane publikacje
- Bruno da Silva F., Gabrovšek B., Korpacz M., Luczkiewicz K., Niewieczerzal S., Sikora M., Sulkowska J.I.
Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks
(2024) Macromolecules, 57 (9), pp. 4599 – 4608
DOI: 10.1021/acs.macromol.3c02479
- Gren B.A., Antczak M., Zok T., Sulkowska J.I., Szachniuk M.
Knotted artifacts in predicted 3D RNA structures
(2024) PLoS Computational Biology, 20 (6 JUNE), art. no. e1011959
DOI: 10.1371/journal.pcbi.1011959
- Dabrowski-Tumanski P., Goundaroulis D., Stasiak A., Rawdon E.J., Sulkowska J.I.
Theta-curves in proteins
(2024) Protein Science, 33 (9), art. no. e5133
DOI: 10.1002/pro.5133
- Rubach P., Sikora M., Jarmolinska A.I., Perlinska A.P., Sulkowska J.I.
AlphaKnot 2.0: A web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models
(2024) Nucleic Acids Research, 52 (W1), pp. W187 – W193
DOI: 10.1093/nar/gkae443
- Tubiana L., Alexander G.P., Barbensi A., Buck D., Cartwright J.H.E., Chwastyk M., Cieplak M., Coluzza I., Čopar S., Craik D.J., Di Stefano M., Everaers R., Faísca P.F.N., Ferrari F., Giacometti A., Goundaroulis D., Haglund E., Hou Y.-M., Ilieva N., Jackson S.E., Japaridze A., Kaplan N., Klotz A.R., Li H., Likos C.N., Locatelli E., López-León T., Machon T., Micheletti C., Michieletto D., Niemi A., Niemyska W., Niewieczerzal S., Nitti F., Orlandini E., Pasquali S., Perlinska A.P., Podgornik R., Potestio R., Pugno N.M., Ravnik M., Ricca R., Rohwer C.M., Rosa A., Smrek J., Souslov A., Stasiak A., Steer D., Sułkowska J., Sułkowski P., Sumners D.W.L., Svaneborg C., Szymczak P., Tarenzi T., Travasso R., Virnau P., Vlassopoulos D., Ziherl P., Žumer S.
Topology in soft and biological matter
(2024) Physics Reports, 1075, pp. 1 – 137
DOI: 10.1016/j.physrep.2024.04.002
- Sikora M., Klimentova E., Uchal D., Sramkova D., Perlinska A.P., Nguyen M.L., Korpacz M., Malinowska R., Nowakowski S., Rubach P., Simecek P., Sulkowska J.I.
Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model
(2024) Protein Science, 33 (7), art. no. e4998
DOI: 10.1002/pro.4998
- Perlinska A.P., Sikora M., Sulkowska J.I.
Everything AlphaFold tells us about protein knots
(2024) Journal of Molecular Biology, 436 (19), art. no. 168715
DOI: 10.1016/j.jmb.2024.168715
- Niemyska W., Mukherjee S., Gren B.A., Niewieczerzal S., Bujnicki J.M., Sulkowska J.I.
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology
(2024) Journal of Molecular Biology, 436 (6), art. no. 168455
DOI: 10.1016/j.jmb.2024.168455
- Zayats V., Sikora M., Perlinska A.P., Stasiulewicz A., Gren B.A., Sulkowska J.I.
Conservation of knotted and slipknotted topology in transmembrane transporters
(2023) Biophysical Journal, 122 (23), pp. 4528 – 4541
DOI: 10.1016/j.bpj.2023.10.031
- Perlinska A.P., Nguyen M.L., Pilla S.P., Staszor E., Lewandowska I., Bernat A., Purta E., Augustyniak R., Bujnicki J.M., Sulkowska J.I.
Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens
(2023) Frontiers in Molecular Biosciences, 10, art. no. 1223830
DOI: 10.3389/fmolb.2023.1223830
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