Ateneo - UPO

The aim of the course is to introduce the student to the main principles about computer simulation of chemical entities (compounds, proteins).

Andreas Kukol, "Molecular Modeling of Proteins", English | 2014 | ISBN: 1493914642. https://link.springer.com/book/10.1007/978-1-4939-1465-4

Nathan Brown, "In Silico Medicinal Chemistry: Computational Methods to Support Drug Design", English | 2015 | ISBN: 978-1-78262-163-8. https://pubs.rsc.org/en/content/ebook/978-1-78262-163-8

1. Knowledge. At the end of the course students will have to know the main methods currently used in the simulation of systems of chemical-biological interest. In particular, they must be aware of the main computational techniques useful both for the calculation of energies and molecular geometries, and for the conformational analysis of small (drugs, endogenous ligands) and macromolecules (proteins and nucleic acids).
2. Ability to apply knowledge. The student must be able to identify the most appropriate procedure to solve some chemical-biological problems that will be proposed during the course. He must also be able to use some basic modeling software to predict the three-dimensional protein structure and the drug-receptor association.

Basic knowledge of general chemistry, organic chemistry, physics and biochemistry.

The course is given with the support of slides, which are given to the students at the beginning of the lessons.
General and specific topics will be introduced, basic concepts will be provided for the understanding of each issue, and discussions with the students will be held.
The topics covered in class will be the subject of exercises/simulations through the use of complex molecular modeling programs.

For further informations, please refer to the course page on D.I.R. at: http://www.dir.uniupo.it
Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities
Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

See the general course information sheet.

Intro to chemoinformatics. Handling compounds structural information. Public database for compounds.

Compound similarity. Ligand-based virtual screening.
Public database of proteins. Handling proteins structural information.
Protein-ligand interactions.
Pharmacophores. Structure-based virtual screening.

At the end of the course the student will have learned the fundamental aspects necessary to correctly simulate the chemical-biological structures.