Carlo Camilloni, Department of Biosciences, University of Milano, Italy
Structural Bioinformatics is an elective course for the Master programmes Molecular Biotechnology and Bioinformatics (MBB) and Quantitative Biology (QB). The aim is to provide a general introduction to different computational approaches related to computational structural biology and biochemistry. This repository contains both the lecture notes and the laboratory exercises. News about the course will be published on the ARIEL website.
- Structures visualisation and analysis
- Molecular Dynamics simulations (including QM)
- Biomolecules Structure Prediction (including docking)
- Advanced topics: integrative structural biology 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 |
|---|---|---|
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Introduction: information about the course | 10/2024 |
| Lecture | Topic | Last Updated |
|---|---|---|
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Structural Biology and Structure Visualisation | 10/2024 |
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A Statistical Mechanics view of Biomolecular Dynamics | 10/2024 |
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Molecular Dynamics simulations: force-fields, algorithms, analysis | 11/2024 |
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Enhanced Sampling Techniques in MD | 10/2024 |
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Markov State Models (by T. Giorgino) | 11/2024 |
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Quantum Chemistry, QM/MM, and simplified models | 11/2024 |
 |
Machine Learning (by T. Giorgino) | 12/2024 |
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Structures Prediction and Molecular Docking | 12/2024 |
 |
Integrative Modelling and Protein Design | 12/2024 |
| Task | Instructions | Report | Last Updated |
|---|---|---|---|
| T01: Biomolecular Structures Visualisation |  |
 |
10/2024 |
| T02: Basic statistical analysis | |
|
10/2024 |
| T03: Molecular Dynamics simulations | |
|
10/2024 |
| T04: More on the analysis of MD simulations | |
|
10/2024 |
| T05: Enhanced sampling and simplified models | |
|
10/2024 |
| T06: Basic DFT simulations | |
|
10/2024 |
| T07: Protein Structure Prediction | |
|
10/2024 |
| T08: Molecular Docking | |
|
10/2024 |
| T09: Protein Design | |
|
12/2024 |
The following publications are to be considered as part of the course and should be studied for 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 2024/2025)
- The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature, Sci. Adv. 2023
- Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor, J. Chem. Inf 2024
- All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions, bioRxiv 2024
- Building predictive Markov State Models of ion channel permeation from Molecular Dynamics, bioRxiv 2024
- Dissected antiporter modules establish minimal proton-conduction elements of the respiratory complex I, Nat. Comm. 2024
- Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models, JCTC 2023
- BindCraft: one-shot design of functional protein binders, bioRxiv 2024
