What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?
T Tuccinardi - Expert opinion on drug discovery, 2021 - Taylor & Francis
The computer-aided drug design field is constituted by a wide range of different approaches
that can be roughly classified as either ligand-or receptor-based techniques. In order to …
that can be roughly classified as either ligand-or receptor-based techniques. In order to …
gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS
MS Valdés-Tresanco… - Journal of chemical …, 2021 - ACS Publications
Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …
most popular methods to estimate binding free energies. This method has been proven to …
Recent developments in free energy calculations for drug discovery
The grand challenge in structure-based drug design is achieving accurate prediction of
binding free energies. Molecular dynamics (MD) simulations enable modeling of …
binding free energies. Molecular dynamics (MD) simulations enable modeling of …
Molecular basis for redox control by the human cystine/glutamate antiporter system xc−
Cysteine plays an essential role in cellular redox homoeostasis as a key constituent of the
tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability …
tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability …
Structure of Mycobacterium tuberculosis cytochrome bcc in complex with Q203 and TB47, two anti-TB drug candidates
S Zhou, W Wang, X Zhou, Y Zhang, Y Lai, Y Tang, J Xu… - Elife, 2021 - elifesciences.org
Pathogenic mycobacteria pose a sustained threat to global human health. Recently,
cytochrome bcc complexes have gained interest as targets for antibiotic drug development …
cytochrome bcc complexes have gained interest as targets for antibiotic drug development …
VAD-MM/GBSA: a variable atomic dielectric MM/GBSA model for improved accuracy in protein–ligand binding free energy calculations
The molecular mechanics/generalized Born surface area (MM/GBSA) has been widely used
in end-point binding free energy prediction in structure-based drug design (SBDD) …
in end-point binding free energy prediction in structure-based drug design (SBDD) …
[HTML][HTML] MS Binding Assays with UNC0642 as reporter ligand for the MB327 binding site of the nicotinic acetylcholine receptor
V Nitsche, G Höfner, J Kaiser, CGW Gertzen, T Seeger… - Toxicology Letters, 2024 - Elsevier
Intoxications with organophosphorus compounds (OPCs) based chemical warfare agents
and insecticides may result in a detrimental overstimulation of muscarinic and nicotinic …
and insecticides may result in a detrimental overstimulation of muscarinic and nicotinic …
Inhibition of VMAT2 by β2-adrenergic agonists, antagonists, and the atypical antipsychotic ziprasidone
Abstract Vesicular monoamine transporter 2 (VMAT2) is responsible for packing monoamine
neurotransmitters into synaptic vesicles for storage and subsequent neurotransmission …
neurotransmitters into synaptic vesicles for storage and subsequent neurotransmission …
Dual A1/A3 Adenosine Receptor Antagonists: Binding Kinetics and Structure− Activity Relationship Studies Using Mutagenesis and Alchemical Binding Free Energy …
M Stampelou, A Suchankova, E Tzortzini… - Journal of Medicinal …, 2022 - ACS Publications
Drugs targeting adenosine receptors (AR) can provide treatment for diseases. We report the
identification of 7-(phenylamino)-pyrazolo [3, 4-c] pyridines L2–L10, A15, and A17 as low …
identification of 7-(phenylamino)-pyrazolo [3, 4-c] pyridines L2–L10, A15, and A17 as low …
Molecular docking, molecular dynamics simulations, and free energy calculation insights into the binding mechanism between vs-4718 and focal adhesion kinase
M Shi, T Chen, S Wei, C Zhao, X Zhang, X Li… - ACS …, 2022 - ACS Publications
Focal adhesion kinase (FAK) is a 125 kDa nonreceptor tyrosine kinase that plays an
important role in many carcinomas. Thus, the targeting of FAK by small molecules is …
important role in many carcinomas. Thus, the targeting of FAK by small molecules is …