Understanding the impact of binding free energy and kinetics calculations in modern drug discovery

VA Adediwura, K Koirala, HN Do, J Wang… - Expert Opinion on Drug …, 2024 - Taylor & Francis
Introduction For rational drug design, it is crucial to understand the receptor-drug binding
processes and mechanisms. A new era for the use of computer simulations in predicting …

[HTML][HTML] QM, molecular docking and molecular dynamics investigation on acidic phospholipase A2 2 protein and acidic phospholipase A2 3 protein with silane …

UM Chandramohan, P Katta, A Prabakaran… - Chemical Physics …, 2024 - Elsevier
Phytochemicals and non-nutritive plant substances can protect humans from various
diseases by possessing anti-inflammatory or anti-disease properties. The Andrographis …

Alchemical approach performance in calculating the ligand-binding free energy

ST Ngo, QM Thai, TH Nguyen, NN Tuan, TNH Pham… - RSC …, 2024 - pubs.rsc.org
Alchemical binding free energy calculations are one of the most accurate methods for
estimating ligand-binding affinity. Assessing the accuracy of the approach over protein …

Molecular structure, vibrational spectral, electron density analysis on linaloe oil and molecular docking efficacy against the therapeutic target on human …

CU Maheswari - Heliyon, 2024 - europepmc.org
Natural traditional medicine extensively uses certain terpenes and gives plants their flavor,
aroma, and color. Treatments for bacterial infections, malaria, and cardiovascular disorders …

[HTML][HTML] The mutual and dynamic role of TSPO and ligands in their binding process: an example with PK-11195

RM Rao, I El Dhaybi, F Cadet, C Etchebest, J Diharce - Biochimie, 2024 - Elsevier
Translocator protein (TSPO) is an 18 kDa transmembrane protein, localized primarily on the
outer mitochondrial membrane. It has been found to be involved in various physiological …

Impact of drying methods on ergosterol content and cholesterol-lowering activity of Ganoderma lucidum

MS Ashikhmina, AA Ostrokhishko, DA Dyagil… - Food Bioscience, 2024 - Elsevier
The development of the food industry is an integral part of the development of our world. In
recent years, there has been a growing interest in food as drugs. Basidiomycetes grown in …

Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations

M Wang, H Jiang, U Ryde - Journal of Chemical Information and …, 2025 - ACS Publications
Alchemical free-energy perturbation (FEP) is an accurate and thermodynamically stringent
way to estimate relative energies for the binding of small ligands to biological …

[HTML][HTML] GPCR oligomerization across classes: A2AR-mediated regulation of mGlu5R activation

U Orzeł, CAV Barreto, S Filipek, IS Moreira - International Journal of …, 2025 - Elsevier
The adenosine A 2A receptor (A 2A R), a class A GPCR, is a known player in neurological
diseases, including Parkinson's disease and Alzheimer's disease, and is also implicated in …

Exploring the impact of the stargazin V143L mutation on the dynamics of the AMPA receptor: stargazin complex

RP Gouveia, CAV Barreto, R Melo… - Frontiers in Cellular …, 2025 - frontiersin.org
Stargazin, a transmembrane AMPAR regulatory protein (TARP), plays a crucial role in
facilitating the transport of AMPA receptors to the cell surface, stabilising their localisation at …

[HTML][HTML] Discovery of Potential Noncovalent Inhibitors of Dehydroquinate Dehydratase from Methicillin-Resistant Staphylococcus aureus through Computational …

C Millán-Pacheco, L Rios-Soto, N Corral-Rodríguez… - Pharmaceuticals, 2023 - mdpi.com
Bacteria resistance to antibiotics is a concerning global health problem; in this context,
methicillin-resistant Staphylococcus aureus (MRSA) is considered as a high priority by the …