Databases and Cheminformatics Fundamentals
A.Y. 2024/2025
Learning objectives
The course aims to introduce and use some databases in chemistry, with particular reference to organic chemistry and to provide students with the basic concepts and the general principles of chemoinformatics.
Expected learning outcomes
Students will acquired the ability to:
· manage and extract chemical information contained in different databases
· read and modify the most common electronic formats of chemical structures (SMILES, SDF, MOL, PDB)
· recognize and calculate the most common molecular descriptors
· build and evaluate and multivariate models
· set up and analyze a conformational analysis calculation
· prepare and set up a virtual screening workflow
· manage and extract chemical information contained in different databases
· read and modify the most common electronic formats of chemical structures (SMILES, SDF, MOL, PDB)
· recognize and calculate the most common molecular descriptors
· build and evaluate and multivariate models
· set up and analyze a conformational analysis calculation
· prepare and set up a virtual screening workflow
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
The lessons will take place synchronously using Microsoft Teams
The material will be available on Ariel (slides)
The material will be available on Ariel (slides)
Course syllabus
The course will include the following topics:
· Linear, two-dimensional and three-dimensional molecular representation in databases searches
· Description and use of chemical databases (SciFinder, CSD, PDB, Reaxys, PubChem, ChEMBL) for molecular structure searches (the type of query: full structure, substructure, and similarity)
· Definition and description of the main ligand-based and structure-based methods applied for the virtual screening of databases:
- pharmacophore definition and generation: the conformational analysis issue
- molecular descriptors: definition and their use in the multivariate analysis methods to build structure-activity models (QSAR)
- molecular docking
- hints to machine learning methods applied to chemoinformatics and drug discovery
· Linear, two-dimensional and three-dimensional molecular representation in databases searches
· Description and use of chemical databases (SciFinder, CSD, PDB, Reaxys, PubChem, ChEMBL) for molecular structure searches (the type of query: full structure, substructure, and similarity)
· Definition and description of the main ligand-based and structure-based methods applied for the virtual screening of databases:
- pharmacophore definition and generation: the conformational analysis issue
- molecular descriptors: definition and their use in the multivariate analysis methods to build structure-activity models (QSAR)
- molecular docking
- hints to machine learning methods applied to chemoinformatics and drug discovery
Prerequisites for admission
Fundamental courses of chemistry of a Bachelor of Science in Chemistry or related fields.
Teaching methods
Traditional lessons. Traditional teaching activities (32 h) will be integrated with computer lessons on the use of chemical databases (16 h) and a computational software.
Teaching Resources
A. Leach and V. Gillet, 'An Introduction to chemoinformatics', Revised Edition Springer 2007
A. Varnek, Tutorials in Chemoinformatics, John Wiley & Sons Ltd 2017
A. Varnek, Tutorials in Chemoinformatics, John Wiley & Sons Ltd 2017
Assessment methods and Criteria
The exam will consist of a written test of 5-6 open questions which aims to verify the preparation of the student on the course contents. The exercises carried out during the practical lessons in the computer laboratory will be also evaluated. Evaluation of the overall grade of the exam +1, 0, -1 (in thirtieths)
CHIM/06 - ORGANIC CHEMISTRY - University credits: 6
Lessons: 48 hours
Professor:
Civera Monica
Shifts:
Turno
Professor:
Civera MonicaProfessor(s)
Reception:
Chemistry Dep., building 5B, 3rd floor, room 3021