2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 1997-2003

83. Maciej Jasiński, Michel Feig, Joanna Trylska, Improved force fields for peptide nucleic acids with optimized backbone torsion parameters. J. Chem. Theory Comput., accepted, 2018

82. Katarzyna Kulczycka-Mierzejewska, Joanna Sadlej, Joanna Trylska, Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin, J. Mol. Model., accepted, 2018

81. Monika Wojciechowska, Marta Dudek, Joanna Trylska, Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA, Biopolymers, 109(4):e23116, 2018

80. Narayana Sabbavarapu, Tomasz Pieńko, Bat-Hen Zalman, Joanna Trylska, Timor Baasov, Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives, Med. Chem. Commun., 9:503-508, 2018

79. Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska, Interactions of 2'-O-methyl Oligoribonucleotides with the RNA Models of the 30S Subunit A-site, PLoS ONE, 13(1):e0191138, 2018

78. Ksenia Maximova, Tom Venken, Nathalie Reuter, Joanna Trylska, D-peptides as inhibitors of PR3-membrane interactions, BBA - Biomembranes, 1860:458-466, 2018

77. Marcin Równicki, Monika Wojciechowska, Aleksandra J. Wierzba, Jakub Czarnecki, Dariusz Bartosik, Dorota Gryko, Joanna Trylska, Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells, Sci. Rep., 7: 7644, 201710.1038/s41598-017-08032-8

76. Marta Kulik, Agnieszka Markowska-Zagrajek, Monika Wojciechowska, Renata Grzela, Tomasz Wituła, Joanna Trylska, Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target, Biochimie, 138:32-42, 2017

75. Tomasz Pieńko, Aleksandra J. Wierzba, Monika Wojciechowska, Dorota Gryko, Joanna Trylska, Conformational dynamics of cyanocobalamin and its conjugates with peptide nucleic acids J. Phys. Chem. B., 121:2968-2979, 2017

74. Marta Dudek, Joanna Trylska, Molecular dynamics simulations of L-RNA involving homo- and heterochiral complexes, J. Chem. Theory Comput., 13:1244-1253, 2017

73. Sapna G. Thoduka, Paul A. Zaleski, Zofia Dąbrowska, Marcin Równicki, Joanna Stróżecka, Anna Górska, Mikołaj Olejniczak, Joanna Trylska, Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides. Biopolymers107:e23004, 2017

72. Joanna Trylska, Marta Kulik, Interactions of aminoglycoside antibiotics with rRNA, Biochem. Soc. Trans., 44(4):987-993, 2016

71. Anna Górska, Agnieszka Markowska-Zagrajek, Marcin Równicki, Joanna Trylska, Scanning of 16S ribosomal RNA for peptide nucleic acid targets, J. Phys. Chem. B120(33):8369-8378, 2016

70. Aleksandra Wierzba, Monika Wojciechowska, Joanna Trylska, Dorota Gryko, Vitamin B12 suitably tailored for disulfide-based conjugation, Bioconjugate Chemistry, 27:189-197, 2016

69. Katarzyna Kulczycka-Mierzejewska, Joanna Trylska, Joanna Sadlej, Conformational space of clindamycin studied by quantum and full-atom molecular dynamics, Journal of Molecular Modeling,22:20, 2016

68. Marta Kulik, Joanna Trylska, Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site, RAIRO-Operations Research, 50:375-386, 2016

67. Anna Górska, Maciej Jasiński, Joanna Trylska, MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids, Nucl. Acids Res., 43(17):e114, 2015

66. Ksenia Maximova, Joanna Trylska, Kinetics of trypsin catalyzed hydrolysis determined by isothermal titration calorimetry, Analytical Biochemistry, 486:24-34, 2015

65. Filip Leonarski, Joanna Trylska, RedMDStream: Parameterization and simulation toolbox for coarse-grained molecular dynamics models, Biophys. J., 108:1843-1847, 2015

64. Joanna Panecka, Jiri Sponer, Joanna Trylska, Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site, Biochimie, 112:96-110, 2015

63. Marta Kulik, Anna M. Goral, Maciej Jasiński, Paulina M. Dominiak, Joanna Trylska, Electrostatic interactions in aminoglycoside-RNA complexes, Biophys. J., 108(3):655-665, 2015 Cover figure

62. Joanna Panecka, Cameron Mura, Joanna Trylska, Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: A molecular dynamics study, PLoS ONE, 9(11): e111811, 2014

61. Agnieszka Markowska-Zagrajek, Marcin Równicki, Joanna Trylska, Inhibition of bacterial translation and growth by antisense peptide nucleic acids and their potential application in biotechnology (in Polish), Advances in Microbiology, 53(3): 255–263, 2014

60. Joanna Panecka, Marek Havrila, Kamila Reblova, Jiri Sponer, Joanna Trylska, The Role of S-turn2 in the Structure, Dynamics and Function of Mitochondrial Ribosomal A-site. A Bioinformatics and Molecular Dynamics Simulation Study, J. Phys. Chem. B, 118: 6687-6701, 2014

59. Marta Dudek, Julia Romanowska, Tomasz Wituła, Joanna Trylska, Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies, Biochimie, 102: 188-202, 2014

58. Filip Leonarski, Joanna Trylska, Modeling Nucleic Acids at the Residue-Level Resolution, in: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes - from bioinformatics to molecular quantum mechanics, Springer, 109-149, 2014

57. Filip Leonarski, Fabio Trovato, Valentina Tozzini, Andrzej Leś, Joanna Trylska, Evolutionary algorithm in the optimization of a coarse-grained force fieldJ. Chem. Theory Comput.9 (11): 4874–4889, 2013

56. Joanna Trylska, Sapna Thoduka, Zofia Dąbrowska, Using sequence-specific oligonucleotides to inhibit bacterial ribosomal RNA, ACS Chem. Biol., 8(6): 1101–1109, 2013

55. Julia Romanowska, Nathalie Reuter, Joanna Trylska, Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymesProteins: Struct. Funct. Bioinf., 81(1):63-80, 2013

54. Julia Romanowska, Krzysztof Nowiński, Joanna Trylska, Determining geometrically stable domains in molecular conformation sets, J. Chem. Theory Comput., 8: 2588−2599, 2012

53. Joanna Panecka, Joanna Trylska, Molecular Dynamics Techniques in the Studies of the Bacterial Ribosome, in: Theory and Applications in Computational Chemistry: The First Decade of the Second Millennium, AIP Conference Proceedings Series, 1456:207-214, 2012

52. Maciej Długosz, Jan Antosiewicz, Paweł Zieliński, Joanna Trylska, Contributions of Far-Field Hydrodynamic Interactions to the Kinetics of Electrostatically-Driven Molecular Association, J. Phys. Chem. B., 116:5437-5447, 2012

51. Karine Voltz, Joanna Trylska, Nicolas Calimet, Jeremy C. Smith, and Joerg Langowski, Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study, Biophys. J., 102: 849-858, 2012

50. Katarzyna Kulczycka-Mierzejewska, Joanna Trylska, Joanna Sadlej, Quantum mechanical studies of lincosamides,  J. Mol. Model., 18:2727–2740, 2012

49. Maciej Długosz, Joanna Trylska, Secondary structures of native and pathogenic Huntingtin N-terminal fragments, J. Phys. Chem. B, 115: 11597–11608, 2011

48. Maciej Jasiński, Maciej Długosz, Joanna Trylska, Molecular dynamics simulations of PNA oligomers, in: I National Conference of Biophysics Students Proceedings, Department of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, AT Group Ltd. 2010, 75 - 84, ISBN 978-83-61026-50-1, 2011

47. Julia Romanowska, Dariusz Ekonomiuk, Joanna Trylska, Computational studies of RNA dynamics and RNA-ligand interactions, in: Methods for Studying Nucleic Acid Drug Interactions, CRC Press, 337-360, ISBN 978-1439839737, 2011

46. Julia Romanowska, J. Andrew McCammon, Joanna Trylska, Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site, PLoS Computational Biology, 7(7):e1002099, 2011

45. Maciej Długosz, Paweł Zieliński, Joanna Trylska, Brownian dynamics simulations on CPU and GPU with BD_BOX, J. Comput. Chem., 32:2734–2744, 2011

44. Maciej Długosz, Gary A. Huber, J. Andrew McCammon, Joanna Trylska, Brownian dynamics study of the association between the 70S ribosome and the elongation factor G, Biopolymers, 95 (9): 616-627, 2011 Cover figure

43. Maciej Długosz, Joanna Trylska, Diffusion in crowded biological environments. Applications of Brownian dynamics, BMC Biophysics, 4:3, 2011 

42. Filip Leonarski, Fabio Trovato, Valentina Tozzini, Joanna Trylska, Genetic Algorithm Optimization of Force Field Parameters. Application to a Coarse-Grained Model of RNA, in: Lecture Notes in Computer Science, Springer, 6623: 147-152, 2011

41. Joanna Panecka, Cameron Mura, Joanna Trylska, Molecular Dynamics of Potential Ribosomal RNA Binders: Single-Stranded Nucleic Acids and some Analogues, J. Phys. Chem. B, 115 (3): 532–546, 2011

40. Katarzyna Kulczycka, Maciej Długosz, Joanna Trylska, Molecular dynamics of ribosomal elongation factors G and Tu, Eur. Biophys. J., 40: 289–303, 2011

39. Joanna Trylska, Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome,  J. Phys.: Condens. Matter, 22: 453101, 2010

38. Joanna Trylska, The Structure and Function of the Ribosome. Nobel Prize in Chemistry 2009, Kosmos, 1-2 (286-287): 9-16, 2010

37. Joanna Trylska, Simulating Activity of the Bacterial Ribosome, Q. Rev. Biophys., 42:301-316, 2009

36. Maciej Długosz, Jan M. Antosiewicz, Joanna Trylska, pH-Dependent Association of Proteins. The Test Case of Monoclonal Antibody HyHEL-5 and its Antigen Hen Egg White Lysozyme, J. Phys. Chem. B, 113:15662-15669, 2009

35. Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska, RedMD - reduced molecular dynamics package, J. Comput. Chem., 30:2364-2373, 2009

34. Maciej Dlugosz, Joanna Trylska, Aminoglycoside Association Pathways with the 30S Ribosomal Subunit, J. Phys. Chem. B, 113:7322-7330, 2009

33. Piotr Setny, Joanna Trylska; Search for Novel Aminoglycoside Derivatives by Combining Fragment-based Virtual Screening and 3D-QSAR Scoring, J. Chem. Inf. Model., 49:390-400, 2009

32. Joanna Trylska, Computational Modeling of the Bacterial 70S Ribosome and Its Subunits, Biotechnologia, 1(84):36-47, 2009

31. Julia Romanowska, Piotr Setny, Joanna Trylska; Molecular dynamics study of the ribosomal A-site, J. Phys. Chem. B., 112:15227-15243, 2008

30. Maciej Dlugosz, Joanna Trylska; Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition, J. Chem. Phys., 129:015103, 2008

29. Maciej Dlugosz, Jan M. Antosiewicz, Joanna Trylska; Association of Aminoglycosidic Antibiotics with the Ribosomal A-site Studied with Brownian Dynamics, J. Chem. Theory Comput., 4:549-559, 2008 Cover figure

28. Magdalena Gruziel, Pawel Grochowski, Joanna Trylska; The Poisson-Boltzmann model for tRNA. Assessment of the calculation set-up and ionic concentration cutoff, J. Comput. Chem., 29:1970-1981, 2008

27. Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Joerg Langowski, Jeremy Smith; Coarse-grained Force Field for the Nucleosome from Self-consistent Multiscaling, J. Comput. Chem., 29:1429-1439, 2008

26. Pawel Grochowski, Joanna Trylska; Continuum Molecular Electrostatics, Salt Effects and Counterion Binding. A Review of the Poisson-Boltzmann Model and its Modifications, Biopolymers, 89:93-113, 2008

25. Marcin Szypowski, Adam Gorecki, Joanna Trylska, RedMD - a New Package for Reduced Molecular Dynamics, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:389-392, ISBN 978-3-9810843-6-8, 2008

24. Katarzyna Kulczycka, Maciej Dlugosz, Joanna Trylska, Internal Dynamics of Elongation Factors G and Tu Studied with All-atom and Coarse-grained Molecular Dynamics, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:277-280, ISBN 978-3-9810843-6-8, 2008

23. Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jeremy Smith, Joerg Langowski, Global Motions in the Nucleosome Explored using a Coarse-grain Model, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:141-144, ISBN 978-3-9810843-6-8, 2008

22. Maciej Dlugosz, Joanna Trylska, Association of Neamine and its Derivative with the Ribosomal A-site RNA, In: From Computational Biophysics to Systems Biology (CBSB08), John von Neumann Institute for Computing, 40:81-84, ISBN 978-3-9810843-6-8, 2008

21. Joanna Trylska, Valentina Tozzini, Chia-en Chang, J. Andrew McCammon; HIV-1 Protease Substrate Binding and Product Release Pathways Explored with Coarse-Grained Molecular Dynamics, Biophys. J., 92:4179-4187, 2007

20. Chia-en Chang, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations, Chem. Biol. & Drug Design, 69:5-13, 2007 Cover figure

19. Valentina Tozzini, Joanna Trylska, Chia-en Chang, J. Andrew McCammon; Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-Grained Model, J. Struct. Biol., 157:606-615, 2007

18. Magdalena Gruziel, Piotr Kmiec, Joanna Trylska, Bogdan Lesyng; Selected Microscopic and Mezoscopic Modelling Tools and Models - an Overview, In: Molecular Materials with Specific Interactions: Modeling and Design, Ed. A. W. Sokalski, Series Title: Challenges and Advances in Chemistry and Physics, Springer, Dordrecht, The Netherlands, 4:203-224, ISBN-10 1-4020- 5371-1 (HB), (2007)

17. Grace Yang, Joanna Trylska, Yitzhak Tor, J. Andrew McCammon; Binding of Aminoglycosidic Antibiotics to the Oligonucleotide A-site Model and 30S Ribosomal Subunit: Poisson-Boltzmann Model, Thermal Denaturation and Fluorescence Studies, J. Med. Chem., 49:5478-5490, 2006

16. Adam Gorecki, Joanna Trylska, Bogdan Lesyng; Causal Relations in Molecular Dynamics Investigated with Multi-Variable Autoregressive Model, Europhys. Lett., 75:503-509, 2006

15. Chia-en Chang, Tongye Shen, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model, Biophys. J., 90:3880-3885, 2006

14. David D. L. Minh, Chia-en Chang, Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics J. Am. Chem. Soc., 128:6006-6007, 2006

13. Kay Hamacher, Joanna Trylska, J. Andrew McCammon; Dependency Map of Proteins in the Small Ribosomal Subunit, PLoS Comp. Biol., 2:0080-0087, 2006

12. Robert Konecny, Joanna Trylska, Florence Tama, Deqiang Zhang, Nathan A. Baker, Charles L. Brooks, III, J. Andrew McCammon; Electrostatic Properties of Cowpea Chlorotic Mottle Virus and Cucumber Mosaic Virus Capsids, Biopolymers, 82:106-120, 2006

11. Joanna Trylska, J. Andrew McCammon, Charles L. Brooks III; Exploring Assembly Energetics of the 30S Ribosomal Subunit Using an Implicit Solvent Approach, J. Am. Chem. Soc., 127:11125-11133, 2005

10. Joanna Trylska, Valentina Tozzini, J. Andrew McCammon; Exploring Global Motions and Correlations in the Ribosome, Biophys. J., 89:1455-1463, 2005

9. Joanna Trylska, Robert Konecny, Florence Tama, Charles L. Brooks III, J. Andrew McCammon; Ribosome motions modulate electrostatic properties, Biopolymers, 74:423-431, 2004 Cover figure

8. Joanna Trylska, Pawel Grochowski, J. Andrew McCammon; The Role of Hydrogen Bonding in the Enzymatic Reaction Catalyzed by HIV-1 Protease Protein Science, 13:513-528, 2004

7. Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski;  Quantum-Classical Molecular Dynamics Simulations in the Studies of the Reaction Catalyzed by HIV-1 Protease In: Simulation in Research and Development, Polish Association for Computer Simulation, p. 269-276, ISBN:83-7365-048-2, 2003

6. Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski; Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease Biophys. J., 83:794-807, 2002

5. Joanna Trylska, Pawel Grochowski, Maciej Geller; Parameterization of the Approximate Valence Bond (AVB) Method to Describe Potential Energy Surface in the Reaction Catalyzed by HIV-1 Protease Int. J. Quant. Chem., 82:86-103, 2001

4. Roman Bogacewicz, Joanna Trylska, Maciej Geller; Ligand design package (LUDI - MSI) applied to known inhibitors of the HIV-1 protease. Test of performance Acta Poloniae Pharmaceutica, 57:25-28, 2000

3. Joanna Trylska, Jan Antosiewicz, Maciej Geller, C. N. Hodge, Ronald Klabe, Martha S. Head, Michael K. Gilson; Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease Protein Science, 8:180-195, 1999

2. Piotr Bala, Maciej Geller, Krzysztof Ginalski, Pawel Grochowski, Joanna Trylska, Bogdan Lesyng; Approximate Valence Bond Method - A Fast Generator of Quantum Potentials for Molecular Simulations In: Modelling and Simulation: A Tool for the Next Millenium, 13th European Simulation Multiconference, June 1-4, 1999, Warsaw, Poland, p. 181-183, Society for Computer Simulation International, 1999

1. Maciej Geller, Joanna Trylska, Jan Antosiewicz; HIV-1 Protease and its Inhibitors In: Theoretical and Computational Methods in Genome Research, Sandor Suhai Plenum Press, p. 237-242, ISBN:030645503X, 1997