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.

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.
Ability to apply knowledge and understanding: The student will be able to apply the knowledge and understanding gained to the recognition of chemical structures in 3D space, the discussion of their interactions, and their graphic representation.
Management of acquired knowledge: The student will be able to express judgments relating to the 3D structures of molecules and proteins, using the necessary tools for the critical evaluation of figures in scientific articles.
Communication skills: The student will be able to explain in an original way a molecule or protein using the software covered in class.
Learning ability: The student will learn to dynamically and independently manage their knowledge of the structure of molecules and proteins.

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

The course consists of lectures with the support of slides provided to the students at the beginning of the course. General and specific topics will be introduced, providing basic concepts for understanding each issue and encouraging discussions with students. A forum section on the course page on D.I.R. (http://www.dir.uniupo.it) will help the discussions.

For further information, 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.

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 to better depict chemical-biological structures.