J. Sarzynska

发表

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

Katarzyna J Purzycka, K. Weeks, Zhichao Miao, 2017, RNA.

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.

Lennart Nilsson, Tadeusz Kulinski, Joanna Sarzynska, 2003, Biophysical journal.

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.

T. Kulinski, L. Nilsson, J. Sarzynska, 2000, Biophysical journal.

AmiRNA Designer - new method of artificial miRNA design.

Jacek Blazewicz, Agnieszka Rybarczyk, Marek Figlerowicz, 2016, Acta biochimica Polonica.

Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair

R. Kierzek, J. Sarzynska, A. Lahiri, 2019, Scientific Reports.

Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA.

J. Sarzynska, A. Lahiri, I. Deb, 2022, Progress in biophysics and molecular biology.

Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3′ terminus

R. Kierzek, J. Sarzynska, Z. Gdaniec, 2018, RNA.

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

Tomasz K. Wirecki, Zhichao Miao, E. Westhof, 2022, International journal of molecular sciences.

RNAspider: a webserver to analyze entanglements in RNA 3D structures

M. Antczak, M. Popenda, J. Sarzynska, 2022, Nucleic Acids Res..

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields

Lennart Nilsson, Joanna Sarzynska, Ansuman Lahiri, 2014, J. Chem. Inf. Model..

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.

J. Šponer, M. Orozco, T. Kulinski, 2009, Journal of chemical theory and computation.

Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Jaroslav Koča, Petr Kulhánek, Tadeusz Kulinski, 2007, Biophysical journal.

Reparameterizations of the χ Torsion and Lennard‐Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines

Joanna Sarzynska, Ansuman Lahiri, Indrajit Deb, 2016, J. Comput. Chem..

Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives

J. Sarzynska, A. Lahiri, I. Deb, 2021, Journal of Computer-Aided Molecular Design.

The model structure of the hammerhead ribozyme formed by RNAs of reciprocal chirality

J. Barciszewski, M. Popenda, J. Sarzynska, 2020, Bioscience reports.

Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space

Nivedita Dutta, Joanna Sarzynska, Ansuman Lahiri, 2020, J. Chem. Inf. Model..

The origin of the high stability of 3′-terminal uridine tetrads: contributions of hydrogen bonding, stacking interactions, and steric factors evaluated using modified oligonucleotide analogs

R. Kierzek, J. Sarzynska, Z. Gdaniec, 2020, RNA.

Ensemble Allosteric Model for the Modified Wobble Hypothesis.

A. Sarkar, J. Sarzynska, A. Lahiri, 2020, The journal of physical chemistry letters.

Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

L. Nilsson, J. Sarzynska, A. Lahiri, 2019, ACS Omega.

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations.

L. Nilsson, J. Sarzynska, A. Lahiri, 2014, Biopolymers.

FTIR study on nucleotide analogues. 1. Spectral characterization of dinucleoside methylphosphonates and dinucleoside 5'-methylenephosphonates in solution and in solid phase.

J. Sarzynska, J. Stawinski, T. Szabo, 1997, Journal of biomolecular structure & dynamics.

Effect of 2-Thiouridine on RNA Conformation

A. Sarkar, J. Sarzynska, A. Lahiri, 2018, Proceedings of the International Conference "Mathematical Biology and Bioinformatics".

Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution

Lennart Nilsson, Tadeusz Kulinski, Joanna Sarzynska, 2007 .

Bioinformatics Study of Structural Patterns in Plant MicroRNA Precursors

J. Sarzynska, M. Szachniuk, A. Mickiewicz, 2017, BioMed research international.

Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA

Jacek Blazewicz, Maciej Milostan, Marek Figlerowicz, 2017, Comput. Biol. Chem..

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro

J. Bujnicki, J. Sarzynska, Karol Kamel, 2017, Scientific Reports.

How bioinformatics resources work with G4 RNAs

Joanna Miskiewicz, Joanna Sarzynska, Marta Szachniuk, 2020, Briefings Bioinform..

LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations

J. Sarzynska, A. Lahiri, I. Deb, 2022, Journal of biomolecular structure & dynamics.

Topology-based classification of tetrads and quadruplex structures

Tomasz Zok, Mariusz Popenda, Joanna Miskiewicz, 2019, Bioinform..

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure.

Tomasz Zok, Marta Szachniuk, Maciej Antczak, 2016, Acta biochimica Polonica.

Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations

Jacek Blazewicz, Maciej Milostan, Tadeusz Kulinski, 2010 .

The influence of the breed and age on the libido of insemination boars

J. Sarzynska, B. Szostak, 2011 .

Conformational transitions of flanking purines in HIV‐1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics

K. Réblová, J. Šponer, T. Kulinski, 2008, Biopolymers.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Feng Ding, Janusz M Bujnicki, Lin Huang, 2020, RNA.

Crystal engineering of cytidine and deoxycytidine sulphates. I. Preparation, and unusual properties.

M. Jaskólski, J. Sarzynska, M. Figlerowicz, 1992 .

Structural and thermodynamic consequences of base pairs containing pseudouridine and N1-methylpseudouridine in RNA duplexes

J. Sarzynska, A. Lahiri, I. Deb, 2023, bioRxiv.

Entanglements of structure elements revealed in RNA 3D models

R. Adamiak, M. Antczak, M. Popenda, 2021, Nucleic acids research.

Parametrization of 2 - aminopurine and purine in charmm all - atom empirical force field

T. Kulinski, J. Sarzynska, K. Kulinska, 2003 .

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Katarzyna J Purzycka, K. Weeks, Zhichao Miao, 2017, RNA.

Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions

Tomasz K. Wirecki, Zhichao Miao, E. Westhof, 2021, bioRxiv.

Dynamics and Stability of GCAA Tetraloops with 2-Aminopurine and Purine Substitutions

T. Kulinski, J. Sarzynska, 2005, Journal of biomolecular structure & dynamics.

Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field

T. Kulinski, J. Sarzynska, 2005 .

RNA tertiary structure prediction using RNAComposer in CASP15

M. Popenda, J. Sarzynska, Maciej Antczak, 2023, Proteins.