Structure-based design of pharmaceuticals requires the ability to predict ligand affinity based on knowledge of structure. The primary term of interest is the binding affinity constant, K, or the free energy of binding, DG8. It is common to attempt to predict DG8 based on empirically derived terms which represent common contributions such as the hydrophobic effect, hydrogen bonding, and conform...

The energetic properties of ternary Zr–Nb–Sn Zirconium-based alloy with concentration dissolved alloying elements ∼ 1 . 5 % are studied by using density functional theory. possibility additions separated different distances to dissolve/segregate in a host matrix is analyzed the help mixing energy and solute–solute binding energy. ability solutes trap single vacancy discussed studying formation ...

Although cellular processes depend on protein-protein interactions, our understanding of molecular recognition between proteins remains far from comprehensive. Protein-protein interfaces are structural and energetic mosaics in which a subset of interfacial residues, called hot spots, contributes disproportionately to the affinity of the complex. These hot-spot residues can be further clustered ...

The speciation of uranyl ions in fulvic acid (FA) and humic acid (HA), based on models of larger sizes, is systematically studied using density functional theory (DFT). Four uranyl binding sites are suggested for FA and based on their energetics, the preferential binding sites are proposed. The computed binding sites include two chelating types, one through the carboxylate group and one via the...

Understanding of protein-ligand interactions is crucial for rational drug design. Binding isotope effects, BIEs, can provide intimate details of specific interactions between individual atoms of an inhibitor and the binding pocket. We have applied multi-scale QM/MM simulations to evaluate binding energetics of a novel triazole-based non-nucleoside inhibitor of HIV-1 reverse transcriptase and to...

Background: Electrostatic interactions are one of the forces guiding binding molecules to proteins. The assessment this interaction through computational approaches makes it possible evaluate energy protein-drug complexes. Objective: Our purpose here is review some methods used calculate electrostatic complexes and explore capacity these for generation new tools drug discovery using abstraction...

The crowded cellular environment can affect biomolecular binding energetics, with specific effects depending on the properties of partners and local environment. Often, crowding are studied particular complexes, which provide system-specific insights but may not comprehensive trends or a generalized framework to better understand how affects energetics involved in molecular recognition. Here, w...