Carlo Camilloni, Department of Biosciences, University of Milano, Italy
Structural Bioinformatics is an elective course offered within the Master’s programmes in Molecular Biotechnology and Bioinformatics (MBB) and Quantitative Biology (QB). The course introduces a range of computational approaches for modeling and designing biomolecular structures, dynamics, and functions. This repository provides both lecture notes and laboratory exercises, while course updates and announcements will be posted on the ARIEL platform.
- Structures visualisation and analysis
- Biomolecules structure prediction
- Molecular dynamics simulations
- Integrative modelling and protein design
Notes : Slides of the lectures in PDF format
Notebooks : Colab Notebooks for the practicals
Data : Additional files needed for the practicals
For each academic year, a snapshot of the repository is saved as a release.
This is how the course will work:
| Lecture | Topic | Last Updated |
|---|---|---|
 | Introduction: information about the course | 10/2025 |
| Lecture | Topic | Last Updated |
|---|---|---|
 | Structural Biology and Structure Visualisation | 10/2025 |
 | A Statistical Mechanics view of Biomolecular Dynamics | 10/2025 |
 | Machine Learning (by T. Giorgino) | 10/2025 |
 | Structures Prediction and Molecular Docking | 10/2025 |
 | Molecular Dynamics simulations: force-fields, algorithms, analysis | 11/2025 |
 | Enhanced Sampling Techniques in MD | 11/2025 |
 | Markov State Models (by T. Giorgino) | 11/2025 |
 | Quantum Chemistry, QM/MM, and simplified models | 12/2025 |
 | Integrative Modelling and Protein Design | 12/2025 |
| Task | Instructions | Report a | Last Updated |
|---|---|---|---|
| T01: Biomolecular Structures Visualisation |  |  | 10/2025 |
| T02: Basic statistical analysis | | | 10/2025 |
| T03: Protein Structure Prediction | | | 10/2025 |
| T04: Molecular Docking | | | 10/2025 |
| T05: Molecular Dynamics simulations | | | 10/2025 |
| T06: More on the analysis of MD simulations | | | 11/2025 |
| T07: Enhanced sampling and simplified models | | | 11/2025 |
| T08: Basic DFT simulations | | | 11/2025 |
| T09: Protein Design | | | 11/2025 |
The following publications are to be considered as part of the course and should be read before the exam.
- Seeing the PDB: Richardson J.S., Richardson R.C., Goodsell D.S. (2021) J. Biol. Chem. 296:100742 https://doi.org/10.1016/j.jbc.2021.100742
- Biomolecular Simulation: A Computational Microscope for Molecular Biology: Dror R.O., et al. (2012) Annu. Rev. Biophys. 41:429-452 https://doi.org/10.1146/annurev-biophys-042910-155245
- Toward the solution of the protein structure prediction problem: Pearce R., Zhang Y. (2021) J. Biol. Chem. 297:100870 https://doi.org/10.1002/anie.200802019
The exam consists of a PowerPoint presentation (max 10 minutes) of a scientific paper from the list below, followed by a few questions on the paper and the methods we have covered in the lectures. Lab reports will also contribute to the final grade. See the introductory slide above for more information.
List of papers: (academic year 2025/2026)
- A cryptic pocket in CB1 drives peripheral and functional selectivity. [https://doi.org/10.1038/s41586-025-08618-7]
- Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. [https://doi.org/10.1016/j.cell.2024.01.034]
- Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. [https://doi.org/10.1371/journal.pcbi.1012180]
- Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment. [https://pubs.acs.org/doi/10.1021/acs.jpcb.5c05178]
- Dynamical buffering of reconfiguration dynamics in intrinsically disordered proteins. [https://www.biorxiv.org/content/10.1101/2025.10.12.681911v2]
- Hydrolysis of the Urethane Bond Catalyzed by Pseudomonas sp. MIS38 Lipase: A QM/MM Mechanistic Insight. [https://pubs.acs.org/doi/10.1021/acscatal.5c03228]
- Curvature Footprints of Transmembrane Proteins in Simulations with the Martini Force Field. [https://pubs.acs.org/doi/10.1021/acs.jpcb.4c01385]
- Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. [https://doi.org/10.1073/pnas.2313360121]
- De novo design of pH-responsive self-assembling helical protein filaments. [https://www.nature.com/articles/s41565-024-01641-1]