Structural Bioinformatics

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.

The main topics covered are:

1. Structures visualisation and analysis
2. Molecular Dynamics simulations (including QM)
3. Biomolecules Structure Prediction (including docking)
4. Advanced topics: integrative structural biology and protein design

The repository is organised as follow:

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.

Academic year 2024-2025:

This is how the course will work:

Lecture	Topic	Last Updated
	Introduction: information about the course	10/2024

Notes:

Lecture	Topic	Last Updated
	Structural Biology and Structure Visualisation	10/2024
	A Statistical Mechanics view of Biomolecular Dynamics	10/2024
	Molecular Dynamics simulations: force-fields, algorithms, analysis	11/2024
	Enhanced Sampling Techniques in MD	10/2024
	Markov State Models (by T. Giorgino)	11/2024
	Quantum Chemistry, QM/MM, and simplified models	11/2024
	Machine Learning (by T. Giorgino)	11/2023
	Structures Prediction and Molecular Docking	12/2023
	Integrative Modelling and Protein Design	01/2024

Practicals:

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			12/2023

Reference Papers:

The following publications are to be considered as part of the course and should be studied for the exam.

1. 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
2. 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
3. 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

Exam:

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)