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KnotProt 2.0: a database of proteins with knots and other entangled structures.
Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sulkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI. Dabrowski-Tumanski P, et al. Among authors: rubach p. Nucleic Acids Res. 2019 Jan 8;47(D1):D367-D375. doi: 10.1093/nar/gky1140. Nucleic Acids Res. 2019. PMID: 30508159 Free PMC article.
Genus for biomolecules.
Rubach P, Zajac S, Jastrzebski B, Sulkowska JI, Sułkowski P. Rubach P, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D1129-D1135. doi: 10.1093/nar/gkz845. Nucleic Acids Res. 2020. PMID: 31584078 Free PMC article.
Topoly: Python package to analyze topology of polymers.
Dabrowski-Tumanski P, Rubach P, Niemyska W, Gren BA, Sulkowska JI. Dabrowski-Tumanski P, et al. Among authors: rubach p. Brief Bioinform. 2021 May 20;22(3):bbaa196. doi: 10.1093/bib/bbaa196. Brief Bioinform. 2021. PMID: 32935829 Free PMC article.
Waterless structures in the Protein Data Bank.
Wlodawer A, Dauter Z, Rubach P, Minor W, Loch JI, Brzezinski D, Gilski M, Jaskolski M. Wlodawer A, et al. Among authors: rubach p. IUCrJ. 2024 Nov 1;11(Pt 6):966-976. doi: 10.1107/S2052252524009928. IUCrJ. 2024. PMID: 39465564 Free PMC article.
AlphaFold predicts novel human proteins with knots.
Perlinska AP, Niemyska WH, Gren BA, Bukowicki M, Nowakowski S, Rubach P, Sulkowska JI. Perlinska AP, et al. Among authors: rubach p. Protein Sci. 2023 May;32(5):e4631. doi: 10.1002/pro.4631. Protein Sci. 2023. PMID: 36960558 Free PMC article.