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 …
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
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 …
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 …
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 …
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 …
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 …
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 …
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 …
has increased significantly. Here, we review recent developments in the methodology for …
Evaluation of DNA–protein complex structures using the deep learning method
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 …
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 …
significant roles in governing biological pathways and mechanisms from a molecular …