- Docking
- Molecular dynamics
- Free energy
- QSAR
- Cheminformatics
Protocols that re‑run.
Step-by-step tutorials pinned to exact software versions, each showing the output you should get. Free browser tools catch the .mdp mistakes that cost a week of simulation time.
- GROMACS
- 2026.3
- ✓ 4 tutorials · 23 Oct
- AutoDock Vina
- 1.2.7
- ✓ 1 tutorial · 23 Oct
- gmx_MMPBSA
- 1.7.0
- ✓ 1 tutorial · 23 Oct
- AmberTools
- 26.0
- ✓ 2 tutorials · 23 Oct
Plate I · Specimen MK1Drag to rotate
§ 01
The 1HSG series
One system, start to finish: HIV‑1 protease with indinavir, from docking pose to binding free energy.
§ 02
All tutorials → Tutorials
Computational chemistry
ISB-0001Chem Redocking with AutoDock Vina 1.2 and Meeko: a reproducible 1HSG walkthrough Prepare receptor and ligand with Meeko, define the box, dock with Vina 1.2.7, and validate by redocking indinavir into HIV-1 protease (PDB 1HSG). Vina 1.2.7 Docking · 7 min ISB-0002Chem Choosing GROMACS .mdp parameters: a stage-by-stage guide for GROMACS 2026 What every line of an EM, NVT, NPT and production .mdp file does, which defaults to trust, and the force-field-specific settings that matter. GROMACS 2026.3 Molecular dynamics · 6 min ISB-0003Chem Common GROMACS errors and how to fix them (2026 edition) Real grompp, pdb2gmx and mdrun error messages from GROMACS 2026.3, what causes each one, and the fix. No -maxwarn shortcuts. GROMACS 2026.3 Troubleshooting · 6 min ISB-0004Chem Protein–ligand MD in GROMACS 2026 with AMBER99SB-ILDN and GAFF2 (ACPYPE): HIV-1 protease + indinavir A tested protein–ligand MD setup in GROMACS 2026.3: GAFF2/AM1-BCC ligand via ACPYPE, topology merging, solvation, ions, EM, NVT, NPT, production and analysis. GROMACS 2026.3 Molecular dynamics · 9 min ISB-0005Chem MM-GBSA and MM-PBSA with gmx_MMPBSA 1.7: a tested workflow and how to read the numbers End-state binding energies from a GROMACS trajectory with gmx_MMPBSA 1.7.0: inputs, GB vs PB, dielectric, decomposition, entropy, and how to read the numbers. gmx_MMPBSA 1.7.0 Free energy · 9 min ISB-0006Chem How to Curate and Classify Bioactivity Data From ChEMBL How a ChEMBL IC50 table for one target becomes a labelled set: one row per molecule, a mean potency, and a class that leaves the uncertain middle out. Data curation · 4 min ISB-0007Chem Using PaDELPy to Generate Molecular Fingerprints for Machine-Learning QSAR Turn a SMILES table into PaDEL fingerprints and a random forest, then score a held-out split with Matthews correlation. The CV number is computed, not assumed. QSAR · 4 min
§ 03
The workbench
Free tools that run entirely in your browser. Nothing you paste is uploaded.
§ 04
How this site works
01
Version-pinned
Each tutorial lists the exact software versions it was checked against (GROMACS, AutoDock Vina, Meeko, AmberTools, gmx_MMPBSA and so on).
02
Cited
Every method links back to the original paper or the official manual.
03
Written by a practitioner
Every page is written, run and checked by Yassir Boulaamane. See about the site, the author page and the editorial & AI-use policy.
§ 05
Who runs the bench
Postdoctoral researcher, computational drug discovery Yassir Boulaamane Postdoctoral researcher at the Universitat Autònoma de Barcelona (InSiliChem), with a PhD in computational drug discovery. Works on molecular docking, molecular dynamics, free energy calculations and machine-learning QSAR. Molecular docking · Molecular dynamics (GROMACS) · MM-PBSA / MM-GBSA · QSAR and machine learning for molecular properties · Drug metabolism (cytochrome P450)
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