[PDF][PDF] New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure

M Antczak, M Popenda, T Zok… - Acta Biochimica …, 2016 - frontierspartnerships.org
RNAComposer is a fully automated, web-interfaced system for RNA 3D structure prediction,
freely available at http://rnacomposer. cs. put. poznan. pl/and http://rnacomposer. ibch …

RNApdbee 2.0: multifunctional tool for RNA structure annotation

T Zok, M Antczak, M Zurkowski, M Popenda… - Nucleic acids …, 2018 - academic.oup.com
In the field of RNA structural biology and bioinformatics, an access to correctly annotated
RNA structure is of crucial importance, especially in the secondary and 3D structure …

Telomerase RNA-based aptamers restore defective myelopoiesis in congenital neutropenic syndromes

E Martínez-Balsalobre, J García-Castillo… - Nature …, 2023 - nature.com
Telomerase RNA (TERC) has a noncanonical function in myelopoiesis binding to a
consensus DNA binding sequence and attracting RNA polymerase II (RNA Pol II), thus …

Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation

S Rinaldi, E Moroni, R Rozza… - Journal of Chemical …, 2024 - ACS Publications
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute
98–99% of the human genome. Non-coding RNAs encompass diverse functional classes …

Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models

J Gumna, M Antczak, RW Adamiak, JM Bujnicki… - International Journal of …, 2022 - mdpi.com
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions,
all of which depend solely on its structure and dynamics. Since the experimental …

ONQUADRO: a database of experimentally determined quadruplex structures

T Zok, N Kraszewska, J Miskiewicz… - Nucleic Acids …, 2022 - academic.oup.com
ONQUADRO is an advanced database system that supports the study of the structures of
canonical and non-canonical quadruplexes. It combines a relational database that collects …

Entanglements of structure elements revealed in RNA 3D models

M Popenda, T Zok, J Sarzynska, A Korpeta… - Nucleic acids …, 2021 - academic.oup.com
Computational methods to predict RNA 3D structure have more and more practical
applications in molecular biology and medicine. Therefore, it is crucial to intensify efforts to …

RNAComposer and RNA 3D structure prediction for nanotechnology

M Biesiada, K Pachulska-Wieczorek, RW Adamiak… - Methods, 2016 - Elsevier
RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of
RNA tertiary structure is fundamental to understand RNA functions beginning with …

RNAloops: a database of RNA multiloops

J Wiedemann, J Kaczor, M Milostan, T Zok… - …, 2022 - academic.oup.com
Motivation Knowledge of the 3D structure of RNA supports discovering its functions and is
crucial for designing drugs and modern therapeutic solutions. Thus, much attention is …

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

M Antczak, M Popenda, T Zok, M Zurkowski… - …, 2018 - academic.oup.com
Motivation Understanding the formation, architecture and roles of pseudoknots in RNA
structures are one of the most difficult challenges in RNA computational biology and …