TL;DR
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 tumors.
Recent developments in QM-based molecular docking and HTD are reviewed, focusing on cases where QM is used explicitly in docking workflows.
A structural database that systematically maps the complete activation trajectories of pharmaceutically relevant targets, encompassing TS, IS, and all connecting conformational ensembles is presented, offering multiple strategic advantages for drug discovery.
This chapter provides an updated overview of the ProBiS tools, which identify binding sites, predict ligand interactions, and analyze conserved water molecules, and enhances the annotation of AlphaFold2-modeled human proteome structures.
FlexAutoDock is an automated cloud-based molecular docking platform that provides a unified environment for protein-ligand docking and large-scale virtual screening, providing researchers with an accessible computational resource for accelerating early-stage drug discovery.
This chapter provides a comprehensive procedure focusing on a combination of structure-based and ligand-based approaches for discovering inhibitors for development of therapies.
An integrated computational strategy involving pharmacophore mapping, molecular docking, molecular dynamics simulations, and density functional theory (DFT) analysis was employed to identify potential SaFtsZ inhibitors, highlighting compound 15 as a computationally predicted scaffold for the development of SaFtsZ-targe...
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