Molecular docking-based computational platform for high-throughput virtual screening

Abstract

Structure-based virtual screening is a key, routine computational method in computer-aided drug design. Such screening can be used to identify potentially highly active compounds, to speed up the progress of novel drug design. Molecular docking-based virtual screening can help find active compounds from large ligand databases by identifying the binding affinities between receptors and ligands. In this study, we analyzed the challenges of virtual screening, with the aim of identifying highly active compounds faster and more easily than is generally possible. We discuss the accuracy and speed of molecular docking software and the strategy of high-throughput molecular docking calculation, and we focus on current challenges and our solutions to these challenges of ultra-large-scale virtual screening. The development of Web services helps lower the barrier to drug virtual screening. We introduced some related web sites for docking and virtual screening, focusing on the development of pre- and post-processing interactive visualization and large-scale computing.

Screening Techniques for Drug Discovery in Alzheimer’s Disease

“…The binding affinity of a large number of compounds with the target macromolecule can be easily evaluated through in silico molecular docking processes. 55 Advancements in protein structural science technologies, such as cryo-electron microscopy and X-ray crystallography, have led to an increasing number of proteins being elucidated in three dimensions. Additionally, the prediction of protein threedimensional structures is achievable through homology modeling.…”

“…In the CADD approach, both structure and ligand-based pharmacophore models can identify molecules with similar activity against a specific target protein. The binding affinity of a large number of compounds with the target macromolecule can be easily evaluated through in silico molecular docking processes …”

Identification of new inhibitors of NS5 from dengue virus using saturation transfer difference (STD-NMR) and molecular docking studies

“…Molecular docking was then performed to predict the features of the ligand-protein complex. 30 3.1 Identication of the protein (NS5)-ligand interactions using (STD)-NMR spectroscopy STD-NMR is a robust technique to identify weak to moderate ligand-receptor interactions. Through spin-spin relaxation, saturation applied on protein resonance diffuses to different residues and might transfer to the protons of ligands that are interacting with these residues.…”

Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening

“…Noteworthily, Zhang et al have developed aweVS, a package that uses multi-layer databases to integrate all docking tasks and dynamically distribute the large list of docking jobs. The VS process is linearly scaled with the available GPU and CPU to efficiently manage billions of ligands, minimizing the input and output loads [149]. Interestingly, the platform can integrate different docking programs, heterogeneous acceleration software, and different hardware, including GPU processors.…”