Contact:

Interdisciplinary Laboratory of Biological Systems Modelling
Center of New Technologies, University of Warsaw
Questions should be addressed to: Joanna Sulkowska (jsulkowska AT cent.uw.edu.pl)

Technical support: Paweł Rubach (prubach AT cent.uw.edu.pl)

When you publish results using the server, please cite the following paper(s):

• Rubach P, Sikora M, Jarmolinska AI, Perlinska AP, Sulkowska JI; AlphaKnot 2.0 - a web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models; Nucleic Acids Research, 2024
• Niemyska W*, Rubach P*, Greń BA, Nguyen ML, Garstka W, Bruno F, Rawdon EJ, Sulkowska JI; AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods; 50(W1), W44-W50.

Publications related to knot proteins and methods of their analysis:

• Perlinska A, Niemyska WG, Gren BA, Bukowicki M, Nowakowski S, Rubach P and Sulkowska UI; AlphaFold predicts novel human proteins with knots; Protein Science (2023), 32(5), e4631.
• Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sułkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI; KnotProt 2.0: a database of proteins with knots and other entangled structures; Nucleic Acids Research (2018), 47(D1), D367-D375.
• Jamroz M, Niemyska W, Rawdon EJ, Stasiak A, Millett KC, Sułkowski P, Sulkowska JI; KnotProt: a database of proteins with knots and slipknots; Nucleic Acids Research (2014), 43(D1), D306-D314.
• Dabrowski-Tumanski P, Rubach P, Niemyska W, Gren BA, Sulkowska JI; Topoly: Python package to analyze topology of polymers; Briefings in Bioinformatics (2021), 22(3).
• Jarmolinska AI, Gambin A, Sulkowska JI; Knot_pull – python package for biopolymer smoothing and knot detection; (2020) Bioinformatics 36(3): 953-955.

Publications related to application of AI methods to investigation/discovery of entanglement of proteins:

• Perlinska A, Niemyska WG, Gren BA, Bukowicki M, Nowakowski S, Rubach P and Sulkowska JI; AlphaFold predicts novel human proteins with knots; Protein Science (2023), 32(5), e4631.
• Niemyska W*, Rubach P*, Greń BA, Nguyen ML, Garstka W, Bruno F, Rawdon EJ, Sulkowska JI; AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods; 50(W1), W44-W50.
• Sikora M, Flapan E, Wong H, Rubach P, Garstka W, Niewieczerzal S, Rawdon EJ, Sulkowska JI; Proteins containing 6-crossing knot types and their folding pathways; bioRxiv, 2023.06. 16.545156.
• Bruno da Silva F, Lewandowska I, Kluza A, Niewieczerzal S, Augustyniak R, Sulkowska JI; First crystal structure of double knotted protein TrmD-Tm1570–inside from degradation perspective; bioRxiv, 2023.03. 13.532328.
• Perlinska AP, Nguyen ML, Pilla SP, Staszor E, Lewandowska I, Bernat A, Putra E, Augustyniak R, Bujnicki JM, Sulkowska JI; Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens; under review.

How to cite