StructBioTools — Computational Structural Biology for Researchers
Computational structural biology

The tools that
drive modern
structure biology

Practical, in-depth tutorials covering everything from molecular docking and MD simulation to PyMOL visualization and Python automation. Written for working researchers.

Explore tutorials ↓ Upcoming courses
73
In-depth tutorials
5
Complete learning pillars
127k
Words of content
100%
Free to read
Five content pillars

Everything a structural biologist needs to compute

01
Molecular docking

The complete guide to molecular docking and virtual screening

AutoDock Vina, GNINA, protein preparation, grid setup, scoring, hit selection, and validated docking workflows — from first principles through publication-ready results.

13 tutorials · ~25,000 words Read pillar →
02
Molecular dynamics

The complete guide to MD simulation with GROMACS

System preparation, force fields, equilibration, production runs, RMSD, RMSF, hydrogen bonds, and MM-GBSA binding energy calculations.

15 tutorials Read pillar →
03
Structure prediction

The complete guide to protein structure prediction and AlphaFold

AlphaFold2, ColabFold, ESMFold, homology modeling, pLDDT interpretation, PAE maps, and using predicted structures for docking and simulation.

15 tutorials Read pillar →
04
PyMOL

The complete PyMOL guide — visualization and publication figures

Essential commands, coloring schemes, surfaces, alignments, protein-ligand visualization, AlphaFold confidence coloring, and publication-quality ray-traced figures.

15 tutorials Read pillar →
05
Python

Python for structural biology — BioPython and MDAnalysis

Parse PDB files, download AlphaFold structures, calculate RMSD and RMSF, analyze trajectories, automate GROMACS analysis, and parse docking results — all in Python.

15 tutorials Read pillar →
Coming soon

Structured courses for researchers who want to go deeper

In development
🔬

Drug Discovery Computational Pipeline

End-to-end virtual screening — target preparation, library docking, hit filtering, ADMET prediction, and MD validation of top compounds.

12 modules · ~8 hours
In development
⚙️

MD Simulation Mastery with GROMACS

From installation through production runs. Force field selection, system setup, analysis pipelines, and publishing-ready results for protein and protein-ligand systems.

10 modules · ~6 hours
In development
🐍

Python for Structural Biology

BioPython and MDAnalysis from scratch — parsing structures, automating analysis, processing large datasets, and building reproducible research pipelines.

8 modules · ~5 hours

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