Tutorials

Understanding how a potential drug candidate behaves in the body—whether it can reach the target site at sufficient concentrations and how long it remains in its bioactive form—constitutes one of the cornerstones of successful drug development. ADMET analysis provides a systematic framework for these evaluations, and in silico models offer valid alternatives, particularly at early stages when access to physical samples is limited.

SwissTargetPrediction is a web-based tool, available online since 2014, designed to predict the most probable protein targets of small molecules. The predictions are based on the principle of similarity through reverse screening.

Molecular docking is an in silico method used to predict how and how strongly a ligand binds to the binding site of a target protein. It is widely used in drug discovery and drug design.

Packmol enables the creation of initial configurations for molecular dynamics simulations by packing molecules into defined regions of space. Various spatial constraints that can be applied to molecules or their atoms facilitate the creation of ordered systems such as layered, spherical or tubular lipid structures.

This tutorial covers the basic principles of the homology modeling method used to predict the three-dimensional structures of proteins and the implementation steps via the SWISS-MODEL tool. The workflow offered by SWISS-MODEL is explained in five basic steps, from entering the target protein sequence to selecting appropriate templates, from building the model to quality assessment.

AlphaFold2 represents a groundbreaking advancement in protein structure prediction, considered one of artificial intelligence's (AI) most...

Avogadro is an advanced molecule editing and visualization tool developed for use in fields such as computational chemistry, molecular...

The PeptideCutter web tool helps predict the cleavage sites of proteases or various chemicals in protein sequences. Protease cutting can...

SwissSimilarity is a user-friendly web tool that allows similarity analysis by comparing the properties of chemical molecules. This tool...

In silico toxicity models aim to support existing in vitro toxicity methods for predicting the toxic effects of chemicals. In this way,...

ProtParam is a powerful web tool that allows the calculation of various biochemical parameters on protein structures and sequences. This...

BIOVIA Discovery Studio Visualizer is a comprehensive guide prepared for the installation of the software that allows the visualization and analysis of molecular structures on Linux (Ubuntu) operating systems. This guide explains in detail the installation of the necessary packages, downloading the software, licensing procedures and adding icons to the desktop.