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DRPS : Course Catalogue : School of Biological Sciences : Postgraduate

Postgraduate Course: Modelling and Measuring Drug/Protein Interactions (PGBI11131)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 11 (Postgraduate) AvailabilityNot available to visiting students
SCQF Credits20 ECTS Credits10
SummaryDrug discovery often involves the development of computer based models that explain/illustrate the details of the molecular interactions involved. This allows the development of better binding compounds. These models can be a 3D structure of the protein/drug complex, a relationship that links structural aspects to activities, or simplified descriptions of the molecules involved that try to capture some basic aspect of the interaction. These models can then be used to widen the pool of available lead compounds or explain why some compounds show unexpected activity. In all of these models a vital aspect is that it is understood where the weaknesses and strengths of the various models lie and how these models may be validated by experiment.
Course description The general idea that a molecular interaction can be modeled in some way and that conclusions can be drawn from that model and tested in some way. A major aspect of the course is to introduce the concept of molecular graphics as a tool to aid in the understanding and analysis of ligand protein interaction. From this the next area is to show that aspects of the forces that drive molecular binding can be derived from the simple analysis of the close atomic interactions made. The concept that compounds that show similar activities to a particular protein, and therefore must have similar profiles leads to molecular similarity in general. While rigorous modelling of the energetics of protein ligand interaction is possible, it is often too time consuming for routine modelling work and the assumption made in simpler models can be outlined. The link can then be made to more complex analysis techniques that can supply the missing binding information. The course will also encompass models of newer biologic drugs and how their binding modes differ from traditional small molecule entities.
Entry Requirements (not applicable to Visiting Students)
Pre-requisites Co-requisites
Prohibited Combinations Other requirements None
Course Delivery Information
Academic year 2024/25, Not available to visiting students (SS1) Quota:  30
Course Start Semester 1
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 200 ( Lecture Hours 12, Seminar/Tutorial Hours 8, Supervised Practical/Workshop/Studio Hours 16, Feedback/Feedforward Hours 2, Formative Assessment Hours 2, Programme Level Learning and Teaching Hours 4, Directed Learning and Independent Learning Hours 156 )
Assessment (Further Info) Written Exam 0 %, Coursework 100 %, Practical Exam 0 %
Additional Information (Assessment) ICA:
Exercise on ligand bound structures (30%)
Essay based on a known drug discovery target (70%)
Feedback Written feedback will be provided for both pieces of ICA.
No Exam Information
Learning Outcomes
On completion of this course, the student will be able to:
  1. Describe the computational approaches in current use for protein modelling and structure-based drug design.
  2. Analyse and critically assess a macromolecular/ ligand interaction.
  3. Describe the use of molecular force field methods in the analysis of and creation of molecular models and understand the use and limitations of homology models.
  4. Understand how various protein/ligand binding experimental approaches work with models to extend understanding of interactions.
  5. Understand the differences in interaction profile of small molecule and biologic drugs.
Reading List
Additional Information
Graduate Attributes and Skills Knowledge and understanding: An understanding of the innate value of a molecular model and how different levels of model details can be related to experimental measurements.
Technical and Practical Skills: The use of molecular graphics as a skill in assessing molecular structure and molecular interactions.
Personal and Intellectual Autonomy: The course requires extensive external reading and ability to integrate this material with taught material and present it effectively.
KeywordsNot entered
Course organiserDr Matthew Nowicki
Course secretaryMiss Fionnuala Nidhonnabhain
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