Simulation Modeling of Biomolecules
A.Y. 2024/2025
Learning objectives
The aim of the course is acquiring a good knowledge of the most important methods of simulation based on classical mechanics that can be applied to biosystems (proteins, peptides, nucleic acids...)
Expected learning outcomes
Attending the course the student will learn the principal methods for simulating biomolecules, in particular molecular dynamics. The student will also become familiar with free energy calculation methods and techniques.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
Basic concepts:
- Basic molecular modeling. Force fields.
- Statistical mechanics review.
- Molecular dynamics.
- Monte Carlo method.
- The sampling problem. Enhanced sampling methods. Parallel tempering.
- Free energy calculation. Thermodynamic perturbation and integration.
- Umbrella sampling. Jarzynski equality based methods.
- Simplified approaches to calculate binding free energies (MM/GBSA, MM/PBSA).
- Analysis of data from molecular simulations.
Applications:
-Force fields for special systems: Alogens and Coordination Compounds.
- Force field-based conformational analysis.
- Molecular docking.
- Protein-protein interactions: how to model them?
- Design of modulators of protein-protein interactions.
- The problem of protein folding. Folding inhibitors drugs.
- Basic molecular modeling. Force fields.
- Statistical mechanics review.
- Molecular dynamics.
- Monte Carlo method.
- The sampling problem. Enhanced sampling methods. Parallel tempering.
- Free energy calculation. Thermodynamic perturbation and integration.
- Umbrella sampling. Jarzynski equality based methods.
- Simplified approaches to calculate binding free energies (MM/GBSA, MM/PBSA).
- Analysis of data from molecular simulations.
Applications:
-Force fields for special systems: Alogens and Coordination Compounds.
- Force field-based conformational analysis.
- Molecular docking.
- Protein-protein interactions: how to model them?
- Design of modulators of protein-protein interactions.
- The problem of protein folding. Folding inhibitors drugs.
Prerequisites for admission
Basic knowledge of math, physics, physical and organic chemistry
Teaching methods
Frontal lessons assisted by the use of slides and integrated by lecture in informatic lab to show some simple software applications.
Teaching Resources
- M.P. Allen, D.J. Tildesley, Computer simulation of liquids.
- A. R. Leach, Molecular Modelling - Principles and Applications, Longman
-Selected papers on specific subjects suggested during the lesseons
- A. R. Leach, Molecular Modelling - Principles and Applications, Longman
-Selected papers on specific subjects suggested during the lesseons
Assessment methods and Criteria
Oral exam. The exam will consist of a discussion (approximately 30 minutes long) which aims to verify the preparation of the student on the course contents. The examination will typically include two or three questions concerning both basic simulation methods and their applications to the study of biomolecules.
CHIM/02 - PHYSICAL CHEMISTRY - University credits: 6
Lessons: 48 hours
Professor:
Pieraccini Stefano
Shifts:
Turno
Professor:
Pieraccini StefanoProfessor(s)
Reception:
On appointment
Teacher's Office (Dipartimento di Chimica - Ground Floor -B Section) or on MS Teams