Difference between revisions of "2025 DOCK GA tutorial 2 with 1XMU"
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== Introduction == | == 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 | ||
== Setup == | == Setup == | ||
Revision as of 14:40, 18 March 2025
Contents
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
