Bioinformatics and molecular modeling

A.A. 2019/2020
Insegnamento per
8
Crediti massimi
64
Ore totali
SSD
BIO/10 CHIM/06 CHIM/08
Lingua
Inglese

Struttura insegnamento e programma

Edizione attiva
Responsabile
Moduli o unità didattiche
Data modeling in biotechnology
BIO/10 - BIOCHIMICA - CFU: 0
CHIM/06 - CHIMICA ORGANICA - CFU: 0
CHIM/08 - CHIMICA FARMACEUTICA - CFU: 0
Lezioni: 24 ore

Molecular mechanics and dynamics
BIO/10 - BIOCHIMICA - CFU: 0
CHIM/06 - CHIMICA ORGANICA - CFU: 0
CHIM/08 - CHIMICA FARMACEUTICA - CFU: 0
Lezioni: 16 ore

Structural bioinformatics
BIO/10 - BIOCHIMICA - CFU: 0
CHIM/06 - CHIMICA ORGANICA - CFU: 0
CHIM/08 - CHIMICA FARMACEUTICA - CFU: 0
Lezioni: 24 ore
Docente: Eberini Ivano

Informazioni sul programma
The teaching unit of Structural Bioinformatics will provide an overview of bioinformatics techniques useful for dealing with the analysis of proteins, the main pharmacological targets and constituents of biotechnological drugs, introducing students to the logic and theoretical bases on which the most used computational approaches are based (3 CFU).
The teaching units of "Molecular modeling: basic methodologies" (3 CFU) and "Computational methodologies in biopharmaceutical development" (3 CFU) aim to provide the student with the knowledge necessary to understand the theoretical foundations and the fields in which computational chemistry applied to drug design can find valid applications both in the academic and industrial fields, so as to learn to critically evaluate the quality of the results and the limits of these methodologies.
Prerequisiti e modalità di esame
It is a prerequisite to have gained at least:
3 ECTS of informatics
3 ECTS of mathematics and physics
4 ECTS of organic chemistry
6 ECTS in biochemistry, molecular biology or clinical biochemistry

The exam will be divided into two parts: an initial practical test and, if the test has a positive result, an oral test based on the verification of the comprehension and elaboration of the program carried out in class.
Structural bioinformatics
Programma
1. Introduction to bioinformatics
2. Genome organization and evolution
3. Databases, archives and information retrieval
4. Substitution matrices, pairwise and multiple alignments, database search and phylogenetic trees
5. Protein structure and architecture
6. Protein structure prediction and validation: comparative modelling, threading and ab initio approaches
7. Introduction to systems biology
Materiale didattico e bibliografia
1. Arthur M. Lesk, Introduction to Bioinformatics, Fourth Edition. Oxford University Press 2014
Molecular mechanics and dynamics
Programma
1. Elements of statistical thermodynamics
2. Introduction to Molecular Mechanics
a. The force fields
b. Solvent models and periodic conditions
c. Geometry optimization

3. Conformational search (CS)
a. Systematic CS methods
b. Stochastic CS methods

4. Molecular Dynamics (MD)
a. The equations of motion and the calculation of a trajectory
b. The microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NPT) ensembles
c. trajectory analysis (energy profiles, RMSD, RMSF, geometrical parameters, hydrogen-bond, cluster analysis, principal component analysis)
d. Applications and limits of MD

5. Enhanced sampling techniques in MD simulations
a. Simulated annealing
b. Umbrella sampling
c. Replica exchange MD
d. Metadynamics
e. Accelerated MD

6. Calculation of free energy in complex systems
a. The potential of mean force (PMF)
b. Alchemical perturbations (Free Energy Perturbation and Thermodynamic Integration)
c. End-point methods (LIE and MM-PBSA)
Periodo
Secondo semestre
Modalità di valutazione
Esame
Giudizio di valutazione
voto verbalizzato in trentesimi
Docente/i
Ricevimento:
Lun - Ven dalle 14.00 alle 17.00 previo appuntamento
Dipartimento di Scienze Farmaceutiche, via Venezian, 21, edificio 5, lato ovest, terzo piano
Ricevimento:
Su appuntamento
Dipartimento di Scienze Farmacologiche e Biomolecolari, Via Giuseppe Balzaretti, 9 - 20133 Milano