Carlo Camilloni, Department of Biosciences, University of Milano, Italy
Structural Bioinformatics is an elective course for the master degrees in Molecular Biotecnology and Bioinformatics (MBB) and Quantitative Biology (QB). The aim is that of providing a general introduction to different computational approaches related to computational structural biology and biochemistry. This repository includes both the notes and the practicals. News about the course are published on the ARIEL web page.
- 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.
Lecture | Topic | Last Updated |
---|---|---|
Introduction: information about the course | 09/2023 | |
Structural Biology and Structure Visualisation | 09/2023 | |
A Statistical Mechanics view of Biomolecular Dynamics | 09/2023 | |
Molecular Dynamics simulations: force-fields, algorithms, analysis | 10/2023 | |
Enhanced Sampling Techniques in MD | 10/2023 | |
Markov State Models (by T. Giorgino) | 11/2023 | |
Quantum Chemistry, QM/MM, and simplified models | 11/2023 | |
Machine Learning (by T. Giorgino) | 2022 | |
Structures Prediction and Molecular Docking | 2022 | |
Integrative Modelling and Protein Design | 2022 |
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
- Principles for Integrative Structural Biology Studies: Rout P.M., Sali A. (2019) Cell 177:1384-1403 https://doi.org/10.1016/j.cell.2019.05.016
The exam consists of a powerpoint presentation (max 10 minutes) of a scientific paper from a list provided below, this will be followed by few questions regarding the paper and the methodologies that we have dealt with in the lectures. Finally we will go through one of the Tasks performed in the lab by looking at the materials you produced.
Papers list: (Updated Jan 2023)
- Structural Basis of AZD9291 Selectivity for EGFR T790M: Yan X., et al. (2020) J. Med. Chem. 63, 8502−8511 https://dx.doi.org/10.1021/acs.jmedchem.0c00891
- Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities: Casalino L., et al. (2022) ACS Cent. Sci. 8, 1646−1663 https://doi.org/10.1021/acscentsci.2c00981
- Ion Conduction Mechanism as a Fingerprint of Potassium Channels: Domene C., et al. (2021) J. Am. Chem. Soc. 143, 12181−12193 https://doi.org/10.1021/jacs.1c04802
- Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV‐1 Protease: Krzeminśka A., et al. (2016) J. Am. Chem. Soc. 138, 16283−16298 https://dx.doi.org/10.1021/jacs.6b06856
- AI-based structure prediction empowers integrative structural analysis of human nuclear pores: Mosalaganti S., et al. (2022) Science 376, eabm9506 https://doi.org/10.1126/science.abm9506
- Molecular Basis of Small-Molecule Binding to α‐Synuclein: Robustelli P., et al. (2022) J. Am. Chem. Soc. 144, 2501−2510 https://doi.org/10.1021/jacs.1c07591
- De novo protein design by deep network hallucination: Anishchenko I., et al. (2021) Nature 600, 547–552 https://doi.org/10.1038/s41586-021-04184-w
- Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution: Scalone E., et al. (2022) PNAS, e2203181119 https://doi.org/10.1073/pnas.2203181119