TL;DR
Theoceptor method can be applied to X-ray crystallography- or cryo-electron microscopy-derived structures, can be applied equally to covalent and noncovalent binders, and can provide excellent predictions for the changes in activity between matched molecular pairs.
Recent developments in QM-based molecular docking and HTD are reviewed, focusing on cases where QM is used explicitly in docking workflows.
Molecular docking is an important step in drug discovery, enabling the evaluation of receptor-ligand affinity while reducing experimental costs and increasing the number of possible tests. However, the high computational cost associated with molecular docking remains a limiting factor that can restrict both the experim...
The central theme, conformational analysis, links on-target potency via pre-organization of the bioactive conformation with physics-based physicochemical property prediction with physics-based physicochemical property prediction, highlighting neutral polarity as a key determinant of permeability and exposure.
This chapter provides an overview, with literature examples, of underexplored interactions that contribute to molecular binding, including weak hydrogen bonding; anion-π and cation-π interactions; Bürgi-Dunitz and tetrel interactions; halogen and chalcogen bonding; and S···π, C···π, O···π, N···π, and amide···π interact...
This chapter describes a structure-based computational approach to perform high-throughput ligand screens of chemical libraries using open-source software programs and illustrates this workflow with the enzymatic molecular target NAD(P)H:quinone oxidoreductase1 (NQO1), which is overexpressed in a number of human solid...
We have compared the performance of 64 different computational methods, based on combined quantum mechanical (QM) and molecular mechanical (QM/MM) or QM-cluster calculations in a continuum solvent, to estimate the acid constant (pK a) of metal-bound ligands in proteins. As a calibration set, we use 12 experimental pK a...
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