M. Popenda

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.

A new molecular mechanism of RNA circularization and the microRNA sponge formation

J. Barciszewski, S. Jurga, M. Popenda, 2020, Journal of biomolecular structure & dynamics.

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches.

Katarzyna J Purzycka, J. Blazewicz, R. Adamiak, 2015, Methods in enzymology.

Automated 3D structure composition for large RNAs

Jacek Blazewicz, Marta Szachniuk, Maciej Antczak, 2012, Nucleic acids research.

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

Jacek Blazewicz, Tomasz Zok, Marta Szachniuk, 2015, BMC Bioinformatics.

2-Methylwyosine, a Nucleoside With Restricted Anti Conformation in the East Region Enforced by Nucleobase Moiety Modification: Synthesis and Conformational Analysis by NMR and Molecular Dynamics

M. Popenda, W. Folkman, B. Golankiewicz, 2012, Nucleosides, nucleotides & nucleic acids.

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..

Spiegelzymes® Mirror-Image Hammerhead Ribozymes and Mirror-Image DNAzymes, an Alternative to siRNAs and microRNAs to Cleave mRNAs In Vivo?

J. Barciszewski, V. Erdmann, F. Mueller, 2014, PloS one.

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

J. Blazewicz, R. Adamiak, M. Antczak, 2015, BMC Bioinformatics.

An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes

Jacek Blazewicz, Piotr Formanowicz, Marta Szachniuk, 2004, J. Comput. Biol..

High salt solution structure of a left-handed RNA double helix.

Mariusz Popenda, Ryszard W Adamiak, R. Adamiak, 2004, Nucleic acids research.

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

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

Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.

R. Adamiak, Z. Dauter, M. Popenda, 1997, Nucleic acids research.

A new, efficient entry to nucleoside 2′,3′-O,O-cyclophosphorothioates

M. Popenda, M. Wenska, J. Stawinski, 2000 .

A New, Efficient Entry to Nucleoside 2′,3′-O,O-Cyclophosphorothioates.

M. Popenda, M. Wenska, J. Stawinski, 2000 .

1H NMR ANALYSIS OF ISOMERIC 2'(3')-O-TRIALKYLSILYL AND 2'(3')-O-METHYL RIBONUCLEOSIDES

R. Adamiak, M. Popenda, J. Milecki, 1994 .

Z-RNA. The synthesis of 2'-O-[13C]methyl- and 5-methyl-analogs of ribo-CGCGCG.

R. Adamiak, M. Popenda, E. Biała, 1993, Acta biochimica Polonica.

ElTetrado: a tool for identification and classification of tetrads and quadruplexes

M. Popenda, M. Szachniuk, T. Zok, 2020, BMC Bioinformatics.

Topology-based classification of tetrads and quadruplex structures

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

RNApdbee 2.0: multifunctional tool for RNA structure annotation

Jacek Blazewicz, Tomasz Zok, Marta Szachniuk, 2018, Nucleic Acids Res..

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

Marek Blazewicz, Marta Szachniuk, Mariusz Popenda, 2007, Nucleic Acids Res..

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

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

An effect of various nitrogen forms used as fertilizer on Lupinus albus L. yield and protein, alkaloid and alpha -galactosides content

M. Popenda, W. Folkman, C. Burbano, 2005 .

RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

Jacek Blazewicz, Tomasz Zok, Marta Szachniuk, 2014, Nucleic Acids Res..

Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint.

Jan Barciszewski, Mariusz Popenda, J. Barciszewski, 2013, The Biochemical journal.

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

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

Flavan-3-ols from seeds ofLupinus angustifolius

M. Popenda, M. Stobiecki, 1994 .

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Edmund K. Burke, Jacek Blazewicz, Marek Blazewicz, 2010, BMC Bioinformatics.

Entanglements of structure elements revealed in RNA 3D models

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

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Feng Ding, Jian Wang, Janusz M Bujnicki, 2015, RNA.

MCQ4Structures to compute similarity of molecule structures

Tomasz Zok, Marta Szachniuk, Mariusz Popenda, 2013, Central European Journal of Operations Research.

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures

R. Adamiak, M. Antczak, M. Popenda, 2018, BMC Bioinform..

RNAssess—a web server for quality assessment of RNA 3D structures

Jacek Blazewicz, Marta Szachniuk, Maciej Antczak, 2015, Nucleic Acids Res..

RNAlyzer—novel approach for quality analysis of RNA structural models

Jacek Blazewicz, Marta Szachniuk, Maciej Antczak, 2013, Nucleic acids research.

Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions.

R. Adamiak, M. Popenda, M Popenda, 1997, Nucleic acids research.

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation

Tomasz Zok, Marta Szachniuk, Maciej Antczak, 2017, Bioinform..

An assignment walk through 3D NMR spectrum

Jacek Blazewicz, Marta Szachniuk, Mariusz Popenda, 2009, 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint.

J. Barciszewski, M. Popenda, M. Szymanski, 2013, The Biochemical journal.

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

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

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures

Tomasz Zok, Marta Szachniuk, Maciej Antczak, 2018, BMC Bioinformatics.

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

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

RNA tertiary structure prediction using RNAComposer in CASP15

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