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List of works by Joanna Trylska

Aminoglycoside association pathways with the 30S ribosomal subunit

scientific article published on May 2009

Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides

scientific article

Antibacterial Peptide Nucleic Acids-Facts and Perspectives

scientific article published on 28 January 2020

Antimicrobial synergy between mRNA targeted peptide nucleic acid and antibiotics in E. coli

scientific article published on 27 July 2018

Artificial Activation of and Toxin-Antitoxin Systems by Antisense Peptide Nucleic Acids as an Antibacterial Strategy

scientific article published in 2018

Association of aminoglycosidic antibiotics with the ribosomal A-site studied with Brownian dynamics

scientific article

Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies

scientific article published on September 2006

Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations

scientific article published in January 2007

Brownian dynamics simulations on CPU and GPU with BD_BOX.

scientific article published on 2 June 2011

Brownian dynamics study of the association between the 70S ribosome and elongation factor G.

scientific article published on 10 March 2011

Causal relations in molecular dynamics from the multi-variate autoregressive model

scientific article published in August 2006

Coarse-grained force field for the nucleosome from self-consistent multiscaling

Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome ⬇️

scientific article published on October 28, 2010

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

scientific article

Computational Methods Used to Explore Transport Events in Biological Systems

scientific article published on 28 March 2019

Conformational Changes of Anoplin, W-MreB<sub>1-9</sub>, and (KFF)<sub>3</sub>K Peptides near the Membranes

scientific article published on 18 December 2020

Conformational Dynamics of Cyanocobalamin and Its Conjugates with Peptide Nucleic Acids.

scientific article

Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

scientific article published on 03 March 2015

Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics

scientific article published on 5 January 2016

Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

scientific article published on February 2008

Contributions of far-field hydrodynamic interactions to the kinetics of electrostatically driven molecular association

scientific article published on 26 April 2012

Crowded environment affects the activity and inhibition of the NS3/4A protease

scientific article published on 24 July 2020

Dependency map of proteins in the small ribosomal subunit

scientific article

Determining Geometrically Stable Domains in Molecular Conformation Sets.

scientific article published on 2 August 2012

Development of bis-ANS-based modified fluorescence titration assay for IFIT/RNA studies

scientific article published on 19 September 2020

Diffusion in crowded biological environments: applications of Brownian dynamics ⬇️

scientific article published on March 2, 2011

Does a conjugation site affect transport of vitamin B12-PNA conjugates into bacterial cells?

scientific article published on 15 November 2018

Electrostatic interactions in aminoglycoside-RNA complexes.

scientific article

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

scientific article published on June 2006

Electrostatic similarity of proteins: application of three dimensional spherical harmonic decomposition

scientific article published on July 2008

Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions

scientific article published on 28 August 2019

Enzyme kinetics in crowded solutions from isothermal titration calorimetry

scientific article published on 12 November 2018

Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field

scientific article published on 21 October 2013

Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach

scientific article published in August 2005

Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives.

scientific article published on 2 February 2018

Exploring global motions and correlations in the ribosome

scientific article

Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli

scientific article published on 01 July 2020

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

article

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

scientific article

Genetic Algorithm Optimization of Force Field Parameters: Application to a Coarse-Grained Model of RNA

article

HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics

scientific article

Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target.

scientific article

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters

scientific article published on 06 June 2018

Inhibition of Escherichia coli Growth by Vitamin B 12 –Peptide Nucleic Acid Conjugates

scientific article published on 10 January 2019

Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site

scientific article published on 19 January 2018

Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies.

scientific article published on 24 April 2014

Interactions of aminoglycoside antibiotics with rRNA.

scientific article published on August 2016

Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study

scientific article

Kinetic analysis of IFIT1 and IFIT5 interactions with different native and engineered RNAs and its consequences for designing mRNA-based therapeutics

scientific article published on 28 October 2019

Kinetics of trypsin-catalyzed hydrolysis determined by isothermal titration calorimetry

scientific article published on 25 June 2015

Ligand design package (Ludi--MSI) applied to known inhibitors of the HIV-1 protease. Test of performance.

scientific article published in November 2000

MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids

scientific article

Modeling Crowded Environment in Molecular Simulations

scientific article published on 11 September 2019

Molecular Dynamics Simulations of l-RNA Involving Homo- and Heterochiral Complexes

scientific article published on 8 February 2017

Molecular dynamics of potential rRNA binders: single-stranded nucleic acids and some analogues

scientific article published on 30 December 2010

Molecular dynamics of ribosomal elongation factors G and Tu.

scientific article published on 9 December 2010

Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease.

scientific article published on August 2002

Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin

scientific article published on 03 July 2018

Molecular dynamics study of the ribosomal A-site.

scientific article

Molecular dynamics techniques in the studies of the bacterial ribosome

scientific article published in 2012

Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides

Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection

scientific article published on 18 February 2021

Peptidomimetic inhibitors targeting the membrane-binding site of the neutrophil proteinase 3

scientific article published on 21 June 2019

Quantum mechanical studies of lincosamides

scientific article published on 25 November 2011

RedMD--reduced molecular dynamics package

scientific article

RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models

scientific article published on April 2015

Ribosome motions modulate electrostatic properties

scientific article published in August 2004

Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study

scientific article published on 6 June 2014

Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets.

scientific article published on 22 April 2016

Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring

scientific article

Secondary Structures of Native and Pathogenic Huntingtin N-Terminal Fragments ⬇️

scientific article published on September 21, 2011

Selected Microscopic and Mezoscopic Modelling Tools and Models – an Overview

scientific article published in 2007

Simulating activity of the bacterial ribosome

scientific article

Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site

scientific article published on 28 March 2016

Targeting Type II Toxin-Antitoxin Systems as Antibacterial Strategies

scientific article published on 04 September 2020

The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff

scientific article

The influence of macromolecular crowding on HIV-1 protease internal dynamics

scientific article published on May 2006

The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease

scientific article published on February 2004

Thermal Stability of Peptide Nucleic Acid Complexes

scientific article published on 20 September 2019

Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease

scientific article

Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques

scientific article published on 19 September 2018

Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA.

scientific article

Towards Catalytic Antibiotics: Redesign of Aminoglycosides To Catalytically Disable Bacterial Ribosomes

scientific article published on 21 December 2018

Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site ⬇️

scientific article published on July 21, 2011

Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study

scientific article published on 21 February 2012

Using sequence-specific oligonucleotides to inhibit bacterial rRNA.

scientific article published on 10 May 2013

Vitamin B-peptide nucleic acids use the BtuB receptor to pass through the Escherichia coli outer membrane

scientific article published on 16 February 2021

Vitamin B12 Suitably Tailored for Disulfide-Based Conjugation.

scientific article published on 22 December 2015

Vitamin B12 as a carrier of peptide nucleic acid (PNA) into bacterial cells

scientific article

Vitamin B12 transports modified RNA into E. coli and S. Typhimurium cells

scientific article published on 01 January 2019

d-Peptides as inhibitors of PR3-membrane interactions.

scientific article published on 10 November 2017

pH-dependent association of proteins. The test case of monoclonal antibody HyHEL-5 and its antigen hen egg white lysozyme

scientific article

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