Dependency Map of Proteins in the Small Ribosomal Subunit. - Kay Hamacher; Joanna Trylska; James Andrew McCammon (PLoS Comput. Biol., 2006)

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

Coarse-grained force field for the nucleosome from self-consistent multiscaling. - Karine Voltz; Joanna Trylska; Valentina Tozzini; Vandana Kurkal-Siebert; Jörg Langowski; Jeremy C. Smith (J. Comput. Chem., 2008)

RedMD - Reduced molecular dynamics package. - Adam Górecki; Marcin Szypowski; Maciej Dlugosz; Joanna Trylska (J. Comput. Chem., 2009)

Search for Novel Aminoglycosides by Combining Fragment-Based Virtual Screening and 3D-QSAR Scoring. - Piotr Setny; Joanna Trylska (J. Chem. Inf. Model., 2009)

Genetic Algorithm Optimization of Force Field Parameters: Application to a Coarse-Grained Model of RNA. - Filip Leonarski; Fabio Trovato; Valentina Tozzini; Joanna Trylska (EvoBio, 2011)

Brownian dynamics simulations on CPU and GPU with BD_BOX. - Maciej Dlugosz; Pawel Zielinski 002; Joanna Trylska (J. Comput. Chem., 2011)

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site. - Julia Romanowska; James Andrew McCammon; Joanna Trylska (PLoS Comput. Biol., 2011)

Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site. - Marta Kulik; Joanna Trylska (RAIRO Oper. Res., 2016)

Computational Methods Used to Explore Transport Events in Biological Systems. - Tomasz Pienko; Joanna Trylska (J. Chem. Inf. Model., 2019)

Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli. - Tomasz Pienko; Joanna Trylska (PLoS Comput. Biol., 2020)

Correction: Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli. - Tomasz Pienko; Joanna Trylska (PLoS Comput. Biol., 2021)

Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease. - Natalia Ostrowska; Michael Feig; Joanna Trylska (PLoS Comput. Biol., 2023)