Prediction of protein–ligand binding affinity via deep learning models

H Wang - Briefings in Bioinformatics, 2024 - academic.oup.com
Accurately predicting the binding affinity between proteins and ligands is crucial in drug
screening and optimization, but it is still a challenge in computer-aided drug design. The …

[HTML][HTML] 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 …

A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape

S Sun, G Rodriguez, G Zhao, JE Sanchez… - Briefings in …, 2024 - academic.oup.com
Abstract The family of Janus Kinases (JAKs) associated with the JAK–signal transducers
and activators of transcription signaling pathway plays a vital role in the regulation of various …

PRA-Pred: Structure-based prediction of protein-RNA binding affinity

K Harini, M Sekijima, MM Gromiha - International Journal of Biological …, 2024 - Elsevier
Understanding crucial factors that affect the binding affinity of protein-RNA complexes is vital
for comprehending their recognition mechanisms. This study involved compiling …

Integrating network pharmacology and in silico analysis deciphers Withaferin-A's anti-breast cancer potential via hedgehog pathway and target network interplay

M Srinivasan, A Gangurde, AY Chandane… - Briefings in …, 2024 - academic.oup.com
This study examines the remarkable effectiveness of Withaferin-A (WA), a withanolide
obtained from Withania somnifera (Ashwagandha), in encountering the mortiferous breast …

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

B Liu, H Shi, HM Al-Hashimi - Current opinion in structural biology, 2021 - Elsevier
Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to
describe their propensities to cycle between different conformations when performing …

Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression

R Mizrahi, O Ostersetzer-Biran - International Journal of Molecular …, 2024 - mdpi.com
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene
organization and expression, particularly at the post-transcriptional level. The primary …

Challenges in structural modeling of RNA-protein interactions

X Liu, Y Duan, X Hong, J Xie, S Liu - Current Opinion in Structural Biology, 2023 - Elsevier
In the past few years, the number of RNA-binding proteins (RBP) and RNA-RBP interactions
has increased significantly. Here, we review recent developments in the methodology for …

Evaluation of DNA–protein complex structures using the deep learning method

C Zeng, Y Jian, C Zhuo, A Li, C Zeng… - Physical Chemistry …, 2024 - pubs.rsc.org
Biological processes such as transcription, repair, and regulation require interactions
between DNA and proteins. To unravel their functions, it is imperative to determine the high …

Integrated modeling of protein and RNA

H Liu, Y Zhao - Briefings in Bioinformatics, 2024 - academic.oup.com
The correct functioning of organisms heavily relies on proteins and RNAs, which hold
significant roles in governing biological pathways and mechanisms from a molecular …