Druggable transient pockets in protein kinases
K Umezawa, I Kii - Molecules, 2021 - mdpi.com
Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity,
adverse off-target effects and inevitable failures in clinical trials. Conventional chemical …
adverse off-target effects and inevitable failures in clinical trials. Conventional chemical …
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 …
Active site sequence representations of human kinases outperform full sequence representations for affinity prediction and inhibitor generation: 3D effects in a 1D …
Recent advances in deep learning have enabled the development of large-scale multimodal
models for virtual screening and de novo molecular design. The human kinome with its …
models for virtual screening and de novo molecular design. The human kinome with its …
DLSSAffinity: protein–ligand binding affinity prediction via a deep learning model
H Wang, H Liu, S Ning, C Zeng, Y Zhao - Physical Chemistry Chemical …, 2022 - pubs.rsc.org
Evaluating the protein–ligand binding affinity is a substantial part of the computer-aided drug
discovery process. Most of the proposed computational methods predict protein–ligand …
discovery process. Most of the proposed computational methods predict protein–ligand …
Strategy toward kinase-selective drug discovery
M Zhang, Y Liu, H Jang, R Nussinov - Journal of Chemical Theory …, 2023 - ACS Publications
Kinase drug selectivity is the ground challenge in cancer research. Due to the structurally
similar kinase drug pockets, off-target inhibitor toxicity has been a major cause for clinical …
similar kinase drug pockets, off-target inhibitor toxicity has been a major cause for clinical …
CavitySpace: a database of potential ligand binding sites in the human proteome
Location and properties of ligand binding sites provide important information to uncover
protein functions and to direct structure-based drug design approaches. However, as …
protein functions and to direct structure-based drug design approaches. However, as …
Protein Kinases and their Inhibitors Implications in Modulating Disease Progression
Protein phosphorylation plays an important role in cellular pathways, including cell cycle
regulation, metabolism, differentiation and survival. The protein kinase superfamily network …
regulation, metabolism, differentiation and survival. The protein kinase superfamily network …
Predicting the activities of drug excipients on biological targets using one-shot learning
Excipients are major components of drugs and are used to improve drug attributes such as
stability and appearance. Excipients approved by the US Food and Drug Administration …
stability and appearance. Excipients approved by the US Food and Drug Administration …
The TAR binding dynamics and its implication in tat degradation mechanism
Human immunodeficiency virus (HIV) is a retrovirus that progressively attacks the human
immune system. It is known that the HIV viral protein Tat recruits the host elongation factor …
immune system. It is known that the HIV viral protein Tat recruits the host elongation factor …
Prediction of allosteric druggable pockets of cyclin-dependent kinases
Cyclin-dependent kinase (Cdk) proteins play crucial roles in the cell cycle progression and
are thus attractive drug targets for therapy against such aberrant cell cycle processes as …
are thus attractive drug targets for therapy against such aberrant cell cycle processes as …