Bioinformatics Tutorials

This repository collects practical tutorials and scripts for structural bioinformatics, molecular docking, molecular dynamics, QM/MM workflows, Linux/HPC routines, and supporting command-line work.

The documentation is written in English and is prepared for publication with GitHub Pages through MkDocs using a Read the Docs style layout.

Documentation Website

The website source lives in docs/ and the navigation is configured in mkdocs.yml.

To preview the site locally:

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

Then open the local URL printed by MkDocs.

To build the static site:

mkdocs build --strict

The build output is written to site/.

GitHub Pages

The repository includes a GitHub Actions workflow at .github/workflows/pages.yml.

After pushing this repository to GitHub:

1. Open the repository settings on GitHub.
2. Go to Pages.
3. Set the source to GitHub Actions.
4. Push to the main branch or run the workflow manually.

GitHub will publish the generated documentation as a GitHub Pages site.

Tutorial Areas

Enzeptional (GT4SD)

Tutorial for enzyme prediction and optimization with Enzeptional (GT4SD), focused on catalytic feasibility and kcat for specific reactions.

Hydrated Docking

Guide for molecular docking with explicit waters using AutoDock Vina, Meeko, and AutoGrid4, focused on hydrated docking in the binding site.

Molecular Dynamics with AMBER

Tutorial for classical protein-ligand molecular dynamics with AMBER, including preparation, minimization, equilibration, production, and analysis, with attention to carbohydrate-containing systems.

Molecular Dynamics with GROMACS

Tutorial for molecular dynamics with GROMACS, covering minimization, equilibration, production, trajectory preprocessing, structural analyses, and free-energy estimation with gmx_MMPBSA.

SLURM for Molecular Simulation Workflows

Practical guide for submitting and monitoring SLURM jobs, focused on GROMACS, AMBER, and MMPBSA workflows in HPC environments.

QM/MM with AMBER and QUICK

Tutorial for QM/MM in AMBER with QUICK, including minimization, equilibration, and production with semiempirical and DFT methods.

DFTB3 QM/MM with AMBER

Tutorial for DFTB3-based QM/MM molecular dynamics in AMBER, focused on sucrose hydrolysis by invertase and mechanism-distance analysis.

QM/MM with GROMACS and CP2K

Protocol for QM/MM with GROMACS + CP2K, including quantum-region definition, index group creation, and GPU-enabled execution.

Scripts

run_md_amber_three_replicates.sh

Script for running minimization, equilibration, and three production replicas in AMBER with pmemd.cuda.

run_cpptraj_replicatas.sh

Script for post-production analysis with cpptraj across multiple replicas, including trajectory centering, ligand RMSD, residue RMSF, radius of gyration, hydrogen bonds, and conformational clustering.

Quick Guides

Docker Commands

Quick reference for useful Docker commands, including images, containers, volumes, environment cleanup, backup, and restoration.

Git Commands

Quick reference for essential Git commands, including configuration, versioning, branches, commits, inspection, and change recovery.

Goal

The goal of this repository is to serve as a practical collection of protocols and commands for:

• molecular docking
• molecular dynamics
• QM/MM calculations
• container usage
• HPC execution
• analysis automation

Notes

The tutorials are intentionally practical and may need adaptation depending on:

• the system under study
• files generated by CHARMM-GUI or related preparation tools
• the target cluster or HPC environment
• installed software versions

Author: Lucas Palmeira