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

78. Ksenia Maximova, Tom Venken, Nathalie Reuter, Joanna Trylska, D-peptides as inhibitors of PR3-membrane interactions, BBA - Biomembranes, under revision 

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, 2017DOI:10.1038/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