2022 Denovo tutorial 2 with PDBID 4ZUD

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De Novo Design

De novo design refers to the process of generating novel ligands in an effort to identify molecules of physiological significance that can be further optimized to become approved drug molecules. The synthesis of thousands of potential drug molecules are done experimentally daily, but with computers, millions of molecules can be computationally modelled and pre-selected for possible synthesis in a fraction of the time it would take to test all possible molecules solely experimentally. With this, scientists are able to direct their attention towards molecules that have the highest probability of imparting a therapeutic effect upon binding to a respective receptor.

This tutorial is the second part of the 2022 DOCK tutorial 2 with PDBID 4ZUD tutorial. You will need the files created in that tutorial to continue with this one!

Make a new directory to organize the files generated in this tutorial:

mkdir 005.denovo

Fragment Library Generation

To create new molecules, we need to begin with the building blocks. For the purposes of speed, we most often use pre-defined molecular fragments that can be arranged/attached in a variety of orientations to create unique structures. Since we have the structure of a ligand that is known to bind the 4ZUD protein, we can generate fragments from that molecule to increase the probability of creating molecules with similar properties to the known ligand.

Focused De Novo Growth

Focused De Novo Rescored