Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data

S Mukherjee, SN Moafinejad, NG Badepally, K Merdas… - Structure, 2024 - cell.com
Recent advancements in RNA three-dimensional (3D) structure prediction have provided
significant insights into RNA biology, highlighting the essential role of RNA in cellular …

Computational modeling of DNA 3D structures: From dynamics and mechanics to folding

ZC Mu, YL Tan, J Liu, BG Zhang, YZ Shi - Molecules, 2023 - mdpi.com
DNA carries the genetic information required for the synthesis of RNA and proteins and
plays an important role in many processes of biological development. Understanding the …

State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction

C Bernard, G Postic, S Ghannay… - NAR Genomics and …, 2024 - academic.oup.com
RNAs are essential molecules involved in numerous biological functions. Understanding
RNA functions requires the knowledge of their 3D structures. Computational methods have …

Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions

X Wang, YL Tan, S Yu, YZ Shi, ZJ Tan - Biophysical Journal, 2023 - cell.com
RNA pseudoknots are a kind of important tertiary motif, and the structures and stabilities of
pseudoknots are generally critical to the biological functions of RNAs with the motifs. In this …

Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops

II Riveros, I Yildirim - Journal of Chemical Theory and …, 2024 - ACS Publications
Access to the three-dimensional structure of RNA enables an ability to gain a more profound
understanding of its biological mechanisms, as well as the ability to design RNA-targeting …

FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures

L Zhou, X Wang, S Yu, YL Tan, ZJ Tan - Biophysical Journal, 2022 - cell.com
Abstract Knowledge of RNA three-dimensional (3D) structures is critical to understanding
the important biological functions of RNAs. Although various structure prediction models …

lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures

S Tarafder, D Bhattacharya - Journal of Chemical Information and …, 2024 - ACS Publications
A scoring function that can reliably assess the accuracy of a 3D RNA structural model in the
absence of experimental structure is not only important for model evaluation and selection …

Modeling Coil–Globule–Helix Transition in Polymers by Self-Interacting Random Walks

E Huang, ZJ Tan - Polymers, 2023 - mdpi.com
Random walks (RWs) have been important in statistical physics and can describe the
statistical properties of various processes in physical, chemical, and biological systems. In …

RNA 3D structure prediction: progress and perspective

X Wang, S Yu, E Lou, YL Tan, ZJ Tan - Molecules, 2023 - mdpi.com
Ribonucleic acid (RNA) molecules play vital roles in numerous important biological
functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled …

Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops

I YILDIRIM, I Riveros - 2023 - chemrxiv.org
Access to the three-dimensional structure of RNA enables an ability to gain a more profound
understanding of its biological mechanisms, as well as the ability to design RNA-targeting …