88. AlphaKnot 2.0 – a web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models
Rubach P, Sikora M, Jarmolinska AI, Perlinska AP, Sulkowska JI
NAR (2024), accepted

87. Topology in soft and biological matter
Tubiana, L., Alexander, G. P., Barbensi, A., Buck, D., Cartwright, J. H. E., Chwastyk, M., … Žumer, S.
Physics Reports (2024), 1075

86. Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks
Bruno da Silva, F., Gabrovšek, B., Korpacz, M., Luczkiewicz, K., Niewieczerzal, S., Sikora, M., & Sulkowska, J. I.
Macromolecules (2024), 57(9)

85. Discovery of a Trefoil Knot in the RydC RNA: Challenging Previous Notions of RNA Topology
W Niemyska, S Mukherjee, B Gren, S Niewieczerzal, JM Bujnicki, JI Sulkowska
Journal of Molecular Biology (2024), 436(6)

84. Knotted artifacts in predicted 3D RNA structures
Gren, B.A., Antczak, M., Zok, T., Sulkowska, J.I. and Szachniuk, M.
On biorXiv since 07.III.2024


83. Conservation of knotted and slipknotted topology in transmembrane transporters
V Zayats, M Sikora, AP Perlinska, A Stasiulewicz, B Gren, JI Sulkowska
Biophysical Journal (2023), 122(23)

82. Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens
ML Nguyen, AP Perlinska, JI Sulkowska, SP Pilla, E Staszor, I Lewandowska, R Augustyniak
Frontiers in Molecular Biosciences (2023), 10

81. AlphaFold predicts novel human proteins with knots
AP Perlinska, WH Niemyska, BA Gren, M Bukowicki, S Nowakowski, P Rubach, JI Sulkowska
Protein Science (2023), 32(5); On biorXiv since 01.I.2022

80. Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation
A Stasiulewicz, A Lesniak, M Bujalska-Zadrożny, T Pawiński, JI Sulkowska
Journal of Chemical Information and Modeling (2023), 63(3)

79. Knot or Not? Sequence-Based Identification of Knotted Proteins With Machine Learning
D Šrámková, M Sikora, D Uchal, E Klimentová, AP Perlinska, ML Nguyen, M Korpacz, R Malinowska, P Rubach, P Šimeček, JI Sulkowska
On biorXiv since 07.IX.2023

78. Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study
M Jedrzejewski, B Belza, I Lewandowska, M Sadlej, AP Perlinska, R Augustyniak, T Christian, Y Hou, M Kalek, JI Sulkowska
Computational and Structural Biotechnology Journal (2023), 21; On biorXiv since 22.III.2023

77. Proteins containing 6-crossing knot types and their folding pathways
M Sikora, E Flapan, H Wong, P Rubach, W Garstka, S Niewieczerzal, EJ Rawdon, JI Sulkowska
On biorXiv since 18.VI.2023

76. First crystal structure of double knotted protein TrmD-Tm1570 – inside from degradation perspective
B da Silva, I Lewandowska, A Kluza, S Niewieczerzal, R Augustyniak, JI Sulkowska
On biorXiv since 14.III.2023


75. Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding
AP Perlinska, A Stasiulewicz, ML Nguyen, K Swiderska, M Zmudzinski, AW Maksymiuk, M Drag, JI Sulkowska
PLoS Computational Biology (2022), 18(11)

74. Identification of CB1 Ligands among Drugs, Phytochemicals and Natural-Like Compounds: Virtual Screening and In Vitro Verification
A Stasiulewicz, A Lesniak, P Setny, M Bujalska-Zadrożny, JI Sulkowska
ACS Chemical Neuroscience (2022), 13(20)

73. AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods
W Niemyska, P Rubach, BA Gren, ML Nguyen, W Garstka, F Bruno da Silva, EJ Rawdon, JI Sulkowska
Nucleic Acids Research (2022), gkac388


72. Lasso Proteins—Unifying Cysteine Knots and Miniproteins
BA Greń*, P Dabrowski-Tumanski*, W Niemyska, JI Sulkowska
Polymers (2021), 13(22), 3988

71. PDBe-KB: collaboratively defining the biological context of structural data
PDBe-KB consortium
Nucleic Acids Research (2021), gkab988

70. Slipknotted and unknotted proteins might share a common ancestor
V Zayats, AI Jarmolinska, B Jastrzebski, S Dunin-Horkawicz, JI Sulkowska
PLoS Computational Biology (2021), 17(10), e1009502

69. SARS-CoV-2 Papain-Like Protease Potential Inhibitors — In Silico Quantitative Assessment
A Stasiulewicz, AW Maksymiuk, ML Nguyen, B Bełza, JI Sulkowska
International Journal of Molecular Sciences (2021), 22(8), 3957


68. GLN: a method to reveal unique properties of lasso type topology in proteins
W Niemyska, KC Millett, JI Sulkowska
Scientific Reports (2020) 10, 15186

67. Topoly: Python package to analyze the topology of polymers
P Dąbrowski-Tumański, P Rubach, W Niemyska, BA Greń, JI Sulkowska
Briefings in Bionformatics (2020) bbaa196

66. Mg2+-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study
AP Perlinska, M Kalek, Y-M Hou, JI Sulkowska
ACS Catalysis (2020) 10(15):8058-8068

65. The Folding of Knotted Proteins: Distinguishing the Distinct behavior of Shallow and Deep Knots
M Piejko, S Niewieczerzal, JI Sulkowska
Israel Journal of Chemistry (2020) 60, 713

64. Restriction of S-adenosylmethionine conformational freedom by knotted binding sites
AP Perlinska*, A Stasiulewicz*, EK Nawrocka, K Kazimierczuk, P Setny, JI Sulkowska
PLoS Computational Biology (2020) 16(5): e1007904.

63. On folding of entangled proteins: knots, lassos, links and theta-curves
JI Sulkowska
Current Opinion in Structural Biology (2020) 60:131-141

62. A Guide to Targeting the Endocannabinoid System in Drug Design
A Stasiulewicz, K Znajdek, M Grudzień, T Pawiński, JI Sulkowska
International Journal of Molecular Sciences (2020) 21, 2778


61. Genus for biomolecules
P Rubach, S Zając, B Jastrzębski, JI Sulkowska, P Sulkowski
Nucleic Acid Research (2019) gkz845

60. Knot_pull – python package for biopolymer smoothing and knot detection
AI Jarmolinska, A Gambin, JI Sulkowska
Bioinformatics (2019) btz644

59. Statistical properties of lasso-shape polymers and their implications for complex lasso proteins function
P Dabrowski-Tumanski, B Gren, JI Sulkowska
Polymers (2019) 11, 4, 707

58. Supercoiling in a protein increases its stability
S Niewieczerzal, JI Sulkowska
Physical Review Letters (2019) 123, 138102

57. PyLink: a PyMOL plugin to identify links
AM Gierut, P Dabrowski-Tumanski, W Niemyska, KC Millett, JI Sulkowska
Bioinformatics (2019) bty1038

56. KnotProt 2.0: A database of proteins with knots and other entangled structures
P Dabrowski-Tumanski, P Rubach, D Goundaroulis, J Dorier, P Sułkowski, KC Millett, EJ Rawdon, A Stasiak, JI Sulkowska
Nucleic Acid Research (2019) 47, D1, Pages D367–D375

55. PconsFam: An interactive database of structure predictions of Pfam families
J Lamb, AI Jarmolinska, M Michel, D Menendez Hurtado, JI Sulkowska, A Elofsson
Journal of Molecular Biology (2019)

54. DCA-MOL – a PyMOL plugin to analyze direct evolutionary couplings
AI Jarmolinska, Q Zhou, JI Sulkowska, F Morcos
Journal of Chemical Information and Modeling (2019) 59, 2, Pages: 625-629

53. Defining and detecting links in chromosomes
S Niewieczerzal, W Niemyska, JI Sulkowska
Scientific Reports (2019) 9:11753

52. Proteins’ knotty problems
AI Jarmolinska, AP Perlinska, R Runkel, B Trefz, HM Ginn, P Virnau, JI Sulkowska
Journal of Molecular Biology (2019) 431, 2, Pages 244-257


51. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting From the Ribosome Exit Channel
P Dabrowski-Tumanski, M Piejko, S Niewieczerzal, S Stasiak, JI Sulkowska
The Journal of Physical Chemistry B (2018) 122, 49, 11616-11625

50. The APS-bracket — a topological tool to classify lasso proteins, RNAs and other tadpole-like structures
P Dabrowski-Tumanski, JI Sulkowska
Reactive and Functional Polymers 132 (2018), Pages 19-25

49. KnotGenom: server to detect entanglement in and between chromosomes
JI Sulkowska, S Niewieczerzal, AI Jarmolinska, JT Siebert, P Virnau, W Niemyska
Nucleic Acids Res. (2018) Volume 46, Issue W1, Pages W17–W24

48. Genus trace reveals the topological complexity and domain structure of biomolecules
S Zajac, C Geary, E Andersen, P Dabrowski-Tumanski, JI Sulkowska, P Sułkowski
Scientific Reports 8.1 (2018): 17537.

47. Entangled proteins: knots, slipknots, links, and lassos
P Sułkowski, JI Sulkowska
Springer Series in Solid-State Sciences 189 (2018)

46. GapRepairer: a server to model a structural gap and validate it using topological analysis
AI Jarmolinska*, M Kadlof*, P Dabrowski-Tumanski, JI Sulkowska
Bioinformatics (2018), bty334

45. The exclusive effects of chaperonin on the behavior of the 52 knotted proteins
Y Zhao*, S Niewieczerzal*, P Dabrowski-Tumanski*, JI Sulkowska
PLoS Computational Biology (2018) 14(3): e1005970


44. To tie or not to tie? That is the question
P Dabrowski-Tumanski, JI Sulkowska
Polymers (2017), 9(9), 454

43. PyLasso – a PyMOL plugin to identify lassos
A Gierut, W Niemyska, P Dabrowski-Tumanski, P Sułkowski, JI Sulkowska
Bioinformatics (2017), btx493

42. Knotting and unknotting proteins in the chaperonin cage: effects of the excluded volume
S Niewieczerzal, JI Sulkowska
PloS One (2017) 12(5) doi: 10.1371/journal.pone.0176744

41. TrmD: A Methyl Transferase for tRNA Methylation With m1G37
YM Hou, R Matsubara, R Takase, I Masuda, JI Sulkowska
The Enzymes (2017): doi: 10.1016/bs.enz.2017.03.003

40. Topological knots and links in proteins
P Dabrowski-Tumanski, JI Sulkowska
PNAS (2017): doi: 10.1073/pnas.1615862114


39. Molecular dynamics and structural comparison approach to understanding the role of the knots in proteins
AP Perlinska, JM Macnar, JI Sulkowska
TASK Quarterly (2016) 20: 373-381

38. Current approaches to disentangle the mystery of knotted protein folding
P Dabrowski-Tumanski, M Sklodowski, JI Sulkowska
TASK Quarterly (2016) 20: 361-371

37. In search of functional advantages of knots in proteins
P Dabrowski-Tumanski, A Stasiak, JI Sulkowska
PLoS One (2016) doi: 10.1371/journal.pone.0165986

36. Complex lasso: new entangled motifs in proteins
W Niemyska, P Dabrowski-Tumanski, M Kadlof, E Haglund, P Sułkowski, JI Sulkowska
Scientific Reports (2016) doi: 10.1038/srep36895

35.LinkProt: database collecting information about biological links
P Dabrowski-Tumanski*, AI Jarmolinska*, W Niemyska*, E Rawdon, KC Millett, JI Sulkowska
Nucleic Acids Res. (2016) doi: 10.1093/nar/gkw976

34. Methyl Transfer by Substrate Signaling from a Knotted Protein Fold
T Christian*, R Sakaguchi*, AP Perlinska*, G Lahoud, T Ito, EA Taylor, S Yokoyama, JI Sulkowska, Y-M Hou
Nature Structural & Molecular Biology (2016) 23: 941-948

33. LassoProt: server to analyze biopolymers with lassos
P Dąbrowski-Tumanski, W Niemyska, P Pasznik, JI Sulkowska
Nucleic Acids Res. (2016), doi: 10.1093/nar/gkw308


32. Prediction of the optimal set of contacts to fold the smallest knotted protein
P Dąbrowski-Tumanski, AI Jarmolińska, JI Sułkowska
J. Phys. Cond. Mat. (2015) 27(35):354109. doi: 10.1088/0953-8984/27/35/354109.


31. KnotProt: a database of proteins with knots and slipknots
M Jamroz, W Niemyska, EJ Rawdon, A Stasiak, KC Millett, P Sułkowski, JI Sulkowska
Nucleic Acids Res. (2014), 43: D306-D314.

30. Pierced Lasso Bundles are a New Class of Knot Motifs
E. Haglund, JI Sulkowska, J.K. Noel, H. Lammert, J.N. Onuchic, PA Jennings
PloS Comput. Biology (2014) 19,10(6):e1003613.

29. Determining Critical Amino Acid contacts for knotted protein
P Dabrowski-Tumanski, S Niewieczerzal, JI Sulkowska
TASK Quarterly (2014) 18 No 3, 323–337.

28. Connecting Thermal and Mechanical Protein (Un)folding Landscapes
L Sun, JK Noel, JI Sulkowska, H Levine, JN Onuchic
Biophys J. 16 (2014), 107(12):2941-52


27. Knot localization in proteins
EJ Rawdon, KC Millett, JI Sulkowska, A Stasiak
Biochemical Society Transactions (2013) 41(2):538-41. doi: 10.1042/BST20120329.

26. Identifying knots in proteins
KC Millett, EJ Rawdon, A Stasiak, JI Sulkowska
Biochemical Society Transactions (2013) 41(2):533-7, doi: 10.1042/BST20120339.

25. Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins
T Andrews, DT Capraro, JI Sulkowska, JN Onuchic, PA Jennings
J. Phys. Chemistry Letters (2013) Jan 3;4(1):180-188.

24. Knotting a Protein in Explicit Solvent
JK Noel, JN Onuchic, JI Sulkowska
J. Phys. Chem. Letters (2013) 4(21), 3570-3573.

23. Knotting pathways in proteins
JI Sulkowska, JK Noel, CA Ramírez-Sarmiento, EJ Rawdon, KC Millett, JN Onuchic
Biochemical Society Transactions (2013) 41(2):523-7, doi: 10.1042/BST20120342.


22. Energy landscape of knotted protein folding
JI Sulkowska*, JK Noel*, JN Onuchic
Proc. Natl. Acad. Sci. USA (2012) doi: 10.1073/pnas.1201804109.

21. Conservation of complex knotting and slipknotting patterns in proteins
JI Sulkowska, EJ Rawdon, KC Millett, JN Onuchic, A Stasiak
Proc. Natl. Acad. Sci (USA), (2012) 109(26): E1715-23.

20. The unique cysteine knot regulates the pleotropic hormone leptin
E Haglund, JI Sulkowska, Z He, Gen-Sheng Feng, P Jennings, JN Onuchic
PloS One (2012) 7(9) e45654.

19. Genomics-aided Structure Prediction (GASP)
JI Sulkowska*, F Marcos*, M Weigt, T Hwa, JN Onuchic
Proc. Natl. Acad. Sci. USA (2012), 109(26): 10340-5.


18. BSDB: the biomolecule stretching database
M Sikora, JI Sulkowska, BS Witkowski, M Cieplak
Nucleic Acids Res. (2011) 39:D443-50. doi: 10.1093/nar/gkq851.

17. Structure based models of biomolecules: stretching of proteins, dynamics of knots, hydrodinamic effects, and indentation of virus capsids
M Cieplak, JI Sulkowska
Springer, A. Koliński, Chapter 8, New York, pp. 179-208, DOI 10.1007/978-1- 4419-6889- 0 (2011).


16. Slipknotting upon native-like loop formation in a trefoil knot protein
JK Noel, JI Sulkowska, JN Onuchic
Proc. Natl. Acad. Sci. USA (2010) 107, 15403.

15. Untying knots in proteins
JI Sulkowska, P Sułkowski, P Szymczak, M Cieplak
J. Am. Chem. Soc. 132 (40) (2010) 13954-13956.

14. A Stevedore’s protein knot
D Bölinger*, JI Sulkowska*, HP Hsu, LA Mirny, M Kardar, JN Onuchic, P Virnau
PLoS Comput Biol. (2010) 6, e1000731.


13. Dodging the crisis of folding proteins with knots
JI Sulkowska, P Sułkowski, JN Onuchic
Proc. Natl. Acad. Sci. USA (2009) 106, 3119-3124, arXiv: 0912.5450 [q-bio].

12. Jamming proteins with slipknots and their free energy landscape
JI Sulkowska, P Sułkowski, JN Onuchic
Phys. Rev. Lett. (2009) 103 268103, arXiv: 1001.0009.

11. On the remarkable mechanostability of scaffoldins and the mechanical clamp motif
A Valbuena, J Oroz, R Hervas, AM Vera, D Rodrigues, A Menedez, JI Sulkowska, M Cieplak, M Carrion-Vazquez
Proc. Natl. Acad. Sci. (2009) 106, 13791.

10. Mechanical strength of 17 134 model proteins and cysteine slipknots motive
M Sikora*, JI Sulkowska*, M Cieplak
PLoS Comput. Biol. (2009) 5, e1000547.

9. Tests of the Structure-Based Models of Proteins
M Cieplak, JI Sulkowska
Act. Phys Polonica A (2009) 115, 441.


8. Stabilizing effect of knots on proteins – How knots influence properties of proteins
JI Sulkowska, P Sułkowski, P Szymczak, M Cieplak
PNAS 105 (2008) 19714-19719, arXiv: 0810.0415 [q-bio].

7. Predicting the Order in Which Contacts Are Broken during Single Molecule Protein Stretching Experiments
JI Sulkowska, A Kloczkowski, TZ Sen, M Cieplak, RL Jernigan
Proteins: Structure, Function, and Bioinformatics (2008) 71, 45-60.

6. Selection of optimal variants of Go-like models of proteins through studies of stretching
JI Sulkowska, M Cieplak
Biophys. J. (2008) 95, 3174.

5. Tightening of knots in proteins
JI Sulkowska, P Sułkowski, P Szymczak, M Cieplak
Phys. Rev. Lett. (2008) 100, 058106.


4. Mechanical Stretching of proteins – A theoretical survey of the Protein Data Bank
JI Sulkowska, M Cieplak
J. Phys. Cond. Mat. (2007) 19, 283201.


3. Correlated fluctuation of microparticles in viscoelastic solutions: quantitative measurement of materials properties by microrheology in the presence of optical traps
M Atakhorrami, JI Sulkowska, KM Addas, G Koenderink, JX Tang, AJ Levine, FC MacKintosh, CF Schmidt
Phys. Rev. E (2006), 73, 061501.


2. Thermal unfolding of proteins
M Cieplak, JI Sulkowska
J. Chem. Phys. (2005) 123, 194908.

1. Chirality and protein folding
JI Kwiecińska, M Cieplak
J. Phys. Cond. Mat. (2005) 17, S1565.


15. Radio TokFM, Radiowa Akademia Nauk – YSF Meeting (1015)

14. „EMBO and Poland”, EMBO Encounters, 28 (2014)

13. „Science that matter”, EMBO, Excellence in life sciences (2014)

12. „Polska badaczka chce rozwiązać zagadkę zawęźlonych białek”, PAP (2013)

11. „Knots and slipknot in protein molecules” Math in the Media, USA

11. Radio TokFM, Radiowa Akademia Nauk – Biophysical Society (2013)

10. “Unraveling the Mysteries of Knotted Proteins” Wired (2012)

9. “Protein Knots Gain New Evolutionary Significance” Science Daily (2012)

8. “Protein folding evolved in knotty puzzle” Futurity (2012)

7. “Knotty proteins present new puzzle” press release in UCSB 2012

6. “Better way to predict how protein fold” Futurity (2012)

5. ”Conservation of complex knotting and slipknotting patterns in proteins” press release at Rice University 2012

4. „How to untie?” J. Am. Chem. Soc., Image Challenge (2011)

3. “Protein folding: knotted or not”, Royal Society of Chemistry – Chemistry World News (2010)

2. “Polscy badacze na tropie tajemnic wezlów w bialkach”, MNiSW – Sukcesy uczonych (2010), PAP – Nauka w Polsce (2010)

1. “Jamming proteins with slipknots and their free energy landscape”, Vir. J. Bio. Phys. Res. 19 (2010)

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