Drug Discovery

How to download small molecules from ZINC database for virtual screening?


It is difficult to manage thousands of compounds altogether while performing virtual high-throughput screening. Compounds databases allow to download molecules in different formats such as the ZINC database [1] allows downloading a batch file that is processed afterward. In this article, we will download small molecules from the ZINC database [1] that can be used in virtual screening. Keep Reading

Prepare receptor and ligand files for docking using Python scripts


Docking software such as Autodock4 [1] and Autodock Vina [2] require input receptor and ligand files in a specific format called pdbqt. Sometimes, preparing files using Autodock Tools (ADT) gives various errors that are not easily understandable. Especially, when we are performing virtual screening (VS), we need to convert a lot of files from pdb to pdbqt format. Converting each file one by one using ADT is a tedious job. Therefore, python scripts provided by Autodock are quite helpful. Keep Reading

Virtual Screening Methodology for Structure-based Drug Designing


Virtual High Throughput Screening (vHTS), also known as Virtual Screening (VS) is one of the essential steps involved in in-silico drug designing. There are several bioinformatics tools that facilitate the virtual screening of thousands of compounds such as GOLD, GLIDE, Autodock Vina, and so on.

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