Bioinformatics Tutorials¶

This site collects practical, reproducible tutorials for structural bioinformatics workflows. It is organized as a technical handbook: each page is focused on a specific task, toolchain, or execution environment.

The documentation is designed for GitHub Pages and uses a Read the Docs style layout with a persistent sidebar, searchable pages, and compact navigation.

Tutorial Areas¶

Area	Use it for
Enzyme design	Enzeptional and GT4SD workflows for catalytic feasibility and activity-oriented predictions.
Docking	Hydrated docking workflows with explicit waters, AutoDock Vina, Meeko, and AutoGrid4.
Molecular dynamics	AMBER and GROMACS protocols for protein-ligand systems, trajectory preparation, and analysis.
QM/MM	AMBER + QUICK and GROMACS + CP2K workflows for hybrid quantum/classical simulations.
HPC	SLURM job submission, monitoring, and practical execution patterns for simulation workflows.
Command-line references	Docker and Git command references for day-to-day project work.

How the Documentation Is Organized¶

The site source lives in docs/.

Tutorial pages are stored in docs/tutorials/ and registered in mkdocs.yml. When a new tutorial README is added to the project, translate or write it in English, place the documentation page under docs/tutorials/, and add it to the navigation.

Local Preview¶

Install the documentation dependencies and start the local server:

python -m venv .venv
. .venv/bin/activate
pip install -r requirements-docs.txt
mkdocs serve

Build the site before publishing:

mkdocs build --strict