2025 DOCK GA tutorial 2 with 1XMU

Introduction

Introduced in DOCK6.10 is the genetic algorithm, a form of de novo drug design that employs molecular evolution (mutations) and an iterative natural selection process. Several fragment-based (requiring a fragment library) mutations, including cross-over, addition, deletion, substitution, and replacement, are used on the provided “parent” molecule(s) to produce a new generation of “off-spring”. Subsequently, the natural selection process uses user-defined variables to exclude “off-spring” with poor scoring (and/or lesser fitness) from being included in the next generation of “parents”.

In this section of the DOCK6.12 tutorial, we will:

• generate a fragment library
• run a genetic algorithm

Set Up

Before we begin, we should create separate directories to guide and organize our workflow.

mkdir 00X_fragLib 
mkdir 00X_algorithm