[HTML][HTML] Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock

Q Xue, X Liu, P Russell, J Li, W Pan, J Fu… - … and Environmental Safety, 2022 - Elsevier
Molecular docking is a widely used method to predict the binding modes of small-molecule
ligands to the target binding site. However, it remains a challenge to identify the correct …

Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics-and knowledge-based approaches

ST Ngo, TH Nguyen, NT Tung, VV Vu… - Physical Chemistry …, 2022 - pubs.rsc.org
Computational approaches, including physics-and knowledge-based methods, have
commonly been used to determine the ligand-binding affinity toward SARS-CoV-2 main …

[HTML][HTML] An accurate and universal protein-small molecule batch docking solution using Autodock Vina

X Che, Q Liu, L Zhang - Results in Engineering, 2023 - Elsevier
As an important theoretical computation method in computer-aided drug design, molecular
docking has significantly shifted the paradigm of drug discovery. As one of the open-source …

Multitargeted Molecular Docking and Dynamic Simulation Studies of Bioactive Compounds from Rosmarinus officinalis against Alzheimer's Disease

FJ Mirza, S Zahid, S Amber, H Jabeen, N Asim… - Molecules, 2022 - mdpi.com
Alzheimer's disease (AD) has been associated with the hallmark features of cholinergic
dysfunction, amyloid beta (Aβ) aggregation and impaired synaptic transmission, which …

Identifying possible AChE inhibitors from drug-like molecules via machine learning and experimental studies

TH Nguyen, PT Tran, NQA Pham, VH Hoang… - ACS …, 2022 - ACS Publications
Acetylcholinesterase (AChE) is one of the most important drug targets for Alzheimer's
disease (AD) treatment. In this work, a machine learning model was trained to rapidly and …

The mechanism of dioscin preventing lung cancer based on network pharmacology and experimental validation

P Xi, Y Niu, Y Zhang, W Li, F Gao, W Gu, F Kui… - Journal of …, 2022 - Elsevier
Abstract Ethnopharmacological relevance Dioscorea nipponica Makino as a Chinese folk
medicine has been used for the treatment of chronic bronchitis, cough, and asthma. Several …

[HTML][HTML] Computational insight into stability-enhanced systems of anthocyanin with protein/peptide

C Xing, P Chen, L Zhang - Food Chemistry: Molecular Sciences, 2023 - Elsevier
Anthocyanins, which belong to the flavonoid group, are commonly found in the organs of
plants native to South and Central America. However, these pigments are unstable under …

Searching for potential inhibitors of SARS-COV-2 main protease using supervised learning and perturbation calculations

TH Nguyen, NM Tam, M Van Tuan, P Zhan, VV Vu… - Chemical Physics, 2023 - Elsevier
Inhibiting the biological activity of SARS-CoV-2 Mpro can prevent viral replication. In this
context, a hybrid approach using knowledge-and physics-based methods was proposed to …

Approaching the dimerization mechanism of small molecule inhibitors targeting PD-L1 with Molecular Simulation

J Liang, B Wang, Y Yang, B Liu, Y Jin - International Journal of Molecular …, 2023 - mdpi.com
Inhibitors blocking the PD-1/PD-L1 immune checkpoint demonstrate impressive anti-tumor
immunity, and small molecule inhibitors disclosed by the Bristol-Myers Squibb (BMS) …

Searching for potential acetylcholinesterase inhibitors: a combined approach of multi-step similarity search, machine learning and molecular dynamics simulations

QM Thai, MQ Pham, PT Tran… - Royal Society Open …, 2024 - royalsocietypublishing.org
Targeting acetylcholinesterase is one of the most important strategies for developing
therapeutics against Alzheimer's disease. In this work, we have employed a new approach …