Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes

C Nithin, P Ghosh, JM Bujnicki - Genes, 2018 - mdpi.com
RNA-protein (RNP) interactions play essential roles in many biological processes, such as
regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing …

In silico approaches to RNA aptamer design

M Hamada - Biochimie, 2018 - Elsevier
RNA aptamers are ribonucleic acids that bind to specific target molecules. An RNA aptamer
for a disease-related protein has great potential for development into a new drug. However …

[HTML][HTML] Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods

TR Patel, G Chojnowski, A Koul, SA McKenna… - Methods, 2017 - Elsevier
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized
the need to develop rapid and accurate methodologies to elucidate the relationship between …

Computational tools to study RNA-protein complexes

S Bheemireddy, S Sandhya, N Srinivasan… - Frontiers in molecular …, 2022 - frontiersin.org
RNA is the key player in many cellular processes such as signal transduction, replication,
transport, cell division, transcription, and translation. These diverse functions are …

Modeling the microscopic electrical properties of thrombin binding aptamer (TBA) for label-free biosensors

E Alfinito, L Reggiani, R Cataldo, G De Nunzio… - …, 2017 - iopscience.iop.org
Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as
drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are …

RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study

C Zhuo, C Zeng, R Yang, H Liu, Y Zhao - International Journal of …, 2023 - mdpi.com
RNA regulates various biological processes, such as gene regulation, RNA splicing, and
intracellular signal transduction. RNA's conformational dynamics play crucial roles in …

Ribonucleoprotein particles: advances and challenges in computational methods

S Dvir, A Argoetti, Y Mandel-Gutfreund - Current Opinion in Structural …, 2018 - Elsevier
Highlights•Many RBPs escape detection by available experimental techniques.•
Developments in computational algorithms enable the prediction of RBPs that do not …

Partner‐specific prediction of RNA‐binding residues in proteins: A critical assessment

Y Jung, Y EL‐Manzalawy, D Dobbs… - Proteins: Structure …, 2019 - Wiley Online Library
RNA‐protein interactions play essential roles in regulating gene expression. While some
RNA‐protein interactions are “specific”, that is, the RNA‐binding proteins preferentially bind …

[PDF][PDF] Homology modeling of the complex between the Repressor of Primer protein and its cognate RNA kissing complex

D Nikolopoulou - 2022 - utopia.duth.gr
The ROP protein is a dimeric protein with an α-helix bundle conformation that is found in
bacteria. ROP protein is involved in the replication regulation mechanism of the …