Ateneo - UPO

The aim of the course is to introduce the student to the main principles of molecular visualization of chemical entities (compounds, proteins).

The course is given with the support of slides.

1. Knowledge and understanding. At the end of the course the student will know and understand the basic concepts of molecular visualization, in particular the student will be instructed on the techniques used to support drug design.
2. Ability to apply knowledge and understanding. The student will be able to apply the knowledge and understanding gained the recognition of chemical structures in 3D space, the discussion of their interactions, and their graphic representation.
3. Management of the knowledge acquired at the end of the expression of judgments relating to the 3D structures of molecules and proteins. In addition, the student will be provided with the necessary tools to apply these skills to the critical evaluation to the figures of scientific articles.
4. Skill in communication, in the know explain, even in an original way, a molecule or protein using the lessons dealt software.
5. Ability to learn and learn how to handle dynamically, and as independent as possible, their own body of knowledge on the structure of molecules and proteins.

Good knowledge in general biology, biochemistry, general pharmacology, and
medicinal chemistry is strongly recommended.

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. A forum section on the course page on D.I.R. (http://www.dir.uniupo.it) will help the discussions.
If the COVID19 emergency continues, the lessons will be carried out by recording and uploading them on Youtube with links in the course on DIR. Upon request, question time will be organized on Google meet.

For further informations, please refer to the course page on D.I.R. at: http://www.dir.uniupo.it

The final exam will be focused on a practical exercise with oral discussion. The exam aims at verifying the ability to create a figure of molecules using the knowledge learned in this course.

The topics will be:
• History of the representation of the molecules
• Database for structures of organic compounds and proteins
• Most popular programs for molecular visualization
• Download, upload and basic display of a model
• Interaction with the molecular models in a virtual space
• Measurement of molecular characteristics
• Surface properties
• Analysis of the protein-inhibitor interactions
• Alignment of 3D structures
• Create high-definition images
• Managing multiple representations (or scenes)
• Creating animations
• Molecular Editing
• Scripting

At the end of the course, the student will acquire theoretical knowledge and understanding about how better depict chemical-biological structures.