Lista de obras - Joanna Trylska - Dominio Público Uruguay

Aminoglycoside association pathways with the 30S ribosomal subunit

artículo científico publicado en 2009

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

artículo científico publicado en 2016

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

artículo científico publicado en 2008

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

artículo científico publicado en 2006

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

artículo científico publicado en 2007

Brownian dynamics simulations on CPU and GPU with BD_BOX.

artículo científico publicado en 2011

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

artículo científico publicado en 2011

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

artículo científico publicado en 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 ⬇️

artículo científico publicado el 28 de octubre de 2010

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

artículo científico publicado en 2012

Computational Methods Used to Explore Transport Events in Biological Systems

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico

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

artículo científico publicado en 2016

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

artículo científico publicado en 2008

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

artículo científico publicado en 2012

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

artículo científico publicado en 2020

Dependency map of proteins in the small ribosomal subunit

artículo científico publicado en 2006

Determining Geometrically Stable Domains in Molecular Conformation Sets.

artículo científico publicado en 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 ⬇️

artículo científico publicado el 2 de marzo de 2011

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

artículo científico publicado en 2018

Electrostatic interactions in aminoglycoside-RNA complexes.

artículo científico publicado en 2015

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

artículo científico publicado en 2006

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

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2013

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

artículo científico publicado en 2005

Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives.

artículo científico publicado en 2018

Exploring global motions and correlations in the ribosome

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 2007

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

artículo científico publicado en 2017

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

artículo científico publicado en 2018

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

artículo científico publicado en 2019

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

artículo científico publicado en 2018

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

artículo científico

Interactions of aminoglycoside antibiotics with rRNA.

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2000

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

artículo científico publicado en 2015

Modeling Crowded Environment in Molecular Simulations

artículo científico publicado en 2019

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

artículo científico publicado en 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.

artículo científico publicado en 2010

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

artículo científico publicado en 2002

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

artículo científico publicado en 2018

Molecular dynamics study of the ribosomal A-site.

artículo científico publicado en 2008

Molecular dynamics techniques in the studies of the bacterial ribosome

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2011

RedMD--reduced molecular dynamics package

artículo científico publicado en 2009

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

artículo científico publicado en 2015

Ribosome motions modulate electrostatic properties

artículo científico publicado en 2004

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2009

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

artículo científico publicado el 21 de septiembre de 2011

Selected Microscopic and Mezoscopic Modelling Tools and Models – an Overview

artículo científico publicado en 2007

Simulating activity of the bacterial ribosome

artículo científico publicado en 2009

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

artículo científico publicado en 2016

Targeting Type II Toxin-Antitoxin Systems as Antibacterial Strategies

artículo científico publicado en 2020

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

artículo científico publicado en 2008

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

artículo científico publicado en 2006

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

artículo científico publicado en 2004

Thermal Stability of Peptide Nucleic Acid Complexes

artículo científico publicado en 2019

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

artículo científico publicado en 1999

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.

artículo científico publicado en 2018

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 ⬇️

artículo científico publicado el 21 de julio de 2011

Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study

artículo científico publicado en 2012

Using sequence-specific oligonucleotides to inhibit bacterial rRNA.

artículo científico publicado en 2013

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

artículo científico publicado en 2021

Vitamin B12 Suitably Tailored for Disulfide-Based Conjugation.

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2019

d-Peptides as inhibitors of PR3-membrane interactions.

artículo científico publicado en 2017

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

artículo científico publicado en 2009

Lista de obras de Joanna Trylska

Aminoglycoside association pathways with the 30S ribosomal subunit

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

Antibacterial Peptide Nucleic Acids-Facts and Perspectives

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

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

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

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

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

Brownian dynamics simulations on CPU and GPU with BD_BOX.

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

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

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 ⬇️

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

Computational Methods Used to Explore Transport Events in Biological Systems

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

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

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

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

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

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

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

Dependency map of proteins in the small ribosomal subunit

Determining Geometrically Stable Domains in Molecular Conformation Sets.

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

Diffusion in crowded biological environments: applications of Brownian dynamics ⬇️

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

Electrostatic interactions in aminoglycoside-RNA complexes.

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

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

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

Enzyme kinetics in crowded solutions from isothermal titration calorimetry

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

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

Exploring eukaryotic versus prokaryotic ribosomal RNA recognition with aminoglycoside derivatives.

Exploring global motions and correlations in the ribosome

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

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

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

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

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

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

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

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

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

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

Interactions of aminoglycoside antibiotics with rRNA.

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

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

Kinetics of trypsin-catalyzed hydrolysis determined by isothermal titration calorimetry

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

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

Modeling Crowded Environment in Molecular Simulations

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

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

Molecular dynamics of ribosomal elongation factors G and Tu.

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

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

Molecular dynamics study of the ribosomal A-site.

Molecular dynamics techniques in the studies of the bacterial ribosome

Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides

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

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

Quantum mechanical studies of lincosamides

RedMD--reduced molecular dynamics package

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

Ribosome motions modulate electrostatic properties

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

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

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

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

Selected Microscopic and Mezoscopic Modelling Tools and Models – an Overview

Simulating activity of the bacterial ribosome

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

Targeting Type II Toxin-Antitoxin Systems as Antibacterial Strategies

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

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

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

Thermal Stability of Peptide Nucleic Acid Complexes