Cited by Identifying RNA-small molecule binding sites using geometric deep learning with language models

The prediction of RNA-small-molecule ligand binding affinity based on geometric deep learning DOI

Wentao Xia,

Jiasai Shu,

Chunjiang Sang

et al.

Computational Biology and Chemistry, Journal Year: 2025, Volume and Issue: 115, P. 108367 - 108367

Published: Jan. 29, 2025

Language: Английский

Citations

Advances and Mechanisms of RNA–Ligand Interaction Predictions DOI

Zhuo Chen, Chengwei Zeng,

Haoquan Liu

et al.

Life, Journal Year: 2025, Volume and Issue: 15(1), P. 104 - 104

Published: Jan. 15, 2025

The diversity and complexity of RNA include sequence, secondary structure, tertiary structure characteristics. These elements are crucial for RNA's specific recognition other molecules. With advancements in biotechnology, RNA-ligand structures allow researchers to utilize experimental data uncover the mechanisms complex interactions. However, determining these complexes experimentally can be technically challenging often results low-resolution data. Many machine learning computational approaches have recently emerged learn multiscale-level features predict Predicting interactions remains an unexplored area. Therefore, studying is essential understanding biological processes. In this review, we analyze interaction characteristics by examining structure. Our goal clarify how specifically recognizes ligands. Additionally, systematically discuss methods predicting guide future research directions. We aim inspire creation more reliable prediction tools.

Language: Английский

Citations

Molecular Dynamics of Apolipoprotein Genotypes APOE4 and SNARE Family Proteins and Their Impact on Alzheimer’s Disease DOI

Yuqing Wang, Xuefeng Liu,

Pengtao Zheng

et al.

Life, Journal Year: 2025, Volume and Issue: 15(2), P. 223 - 223

Published: Feb. 2, 2025

Alzheimer's disease is a chronic neurodegenerative disorder characterized by progressive memory loss and significant impact on quality of life. The APOE ε4 allele major genetic contributor to AD pathogenesis, with synaptic dysfunction being central hallmark in its pathophysiology. While the role APOE4 reducing SNARE protein levels has been established, underlying molecular mechanisms this interaction remain obscure. Our research employs dynamics simulations analyze interactions between APOE3 isoforms proteins VAMP2, SNAP25, SYNTAXIN1, which play crucial roles presynaptic membrane. findings reveal that significantly destabilizes complex, suppresses structural dynamics, reduces hydrogen bonding, consequently partially hindering neurotransmitter release-a very likely discovery for elucidating disease. We identified exhibits diminished affinity complex comparison APOE3. This observation suggests may modulating stability potentially impacting progression occurrence through free energy analysis. work highlights perturbations function mediated APOE4, offer novel insights into underpinnings AD. By interplay our study not only enhances comprehension AD's pathology but also paves way devising innovative therapeutic interventions, such as targeting APOE4-SNARE or restore release.

Language: Английский

Citations

Identifying RNA-small molecule binding sites using geometric deep learning with language models DOI

Weimin Zhu, Xiaohan Ding, Hong‐Bin Shen

et al.

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 169010 - 169010

Published: Feb. 1, 2025

Language: Английский

Citations