Computational Biology
This course gives an introduction to molecular computational biology and to the rational design of proteins using computational techniques. The arguments of the course include: molecular dynamis simulation techniques and advanced protein bioinformatics concepts. At the end of the course the student should be able to: - Deep and critical understanding of a scientific article where computational techniques are used - Introduce (in silico) mutants able to affect the protein structure and/or function - Prepare and run molecular dynamis simulations.
Part A – Bioinformatics
− Advanced Structural Bioinformatics
- Thermodynamic basis of the stability of folded biomolecular structure
− Molecular basis of human perception
Part B – Molecular Modeling
− Basic elements of molecular modeling
− Electrostatic modeling
− Energy minimization based on force fields
− Molecular dynamics: solution by using the open source NAMD and/or Gromacs codes
− Conformational analysis
Part C – Ligand-prtoein interactions
− Protein assembly (protein-protein complexes, protein-protein interactions in protein dimers, crystals): protein-protein docking algorithms and programs
− Ligand Protein interaction: docking algorithms and programs
− Projects: Drug and/or protein design
| Reference books | |||||
| Author | Title | Publisher | Year | ISBN | Note |
| Stefano Pascarella e Alessandro Paiardini | Bioinformatica | Zanichelli | 2011 | 9788808062192 | |
| Frishman, D., Valencia, Alfonso | Modern Genome Annotation | Springer | 2008 | ||
Written.
The examination is divide in two parts: the first consists in the presentation (in groups) of a scientific article in which state of the arte techniques are used.
The second part is a written examination with open questions regarding the arguments of the course.
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Verona University
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