CHY8830 : Molecular Simulations and Computer-aided Drug Design (CADD) (Inactive)
- Inactive for Year: 2022/23
- Module Leader(s): Dr Agnieszka Bronowska
- Lecturer: Dr Daniel Cole
- Owning School: Natural and Environmental Sciences
- Teaching Location: Newcastle City Campus
Semesters
| Semester 2 Credit Value: | 10 |
| ECTS Credits: | 5.0 |
Aims
The second block will focus on molecular docking calculations, applied to iterative lead optimization and to high-throughput virtual screening. The concept of scoring functions will be introduced. Students will learn how to interpret the results and how to assess the methodology. Limitations of docking calculations will be discussed and accompanied by case studies.
The third thematic block will cover an introduction to some more advanced molecular simulation methods, elements of thermodynamics and statistical mechanics, and advanced sampling techniques. The aim is to show students the applicability, advantages and limitations of all these methods and to give them an idea about which methods and techniques to start out with when initiating their own research project.
Outline Of Syllabus
Enhanced sampling techniques and multiscale methods. Key concepts of quantum mechanics (QM). QM/MM simulations. Thermodynamics and free energy methods. Case studies in molecular simulations.
Molecular docking and structure-based design methods in CADD
Molecular docking and virtual screening. High-throughput virtual screening. Hit detection. Hit to lead. Lead optimisation. Fragment growth and scaffold-hopping. Binding site identification. Case studies in structure-guided drug design.
Teaching Methods
Teaching Activities
| Category | Activity | Number | Length | Student Hours | Comment |
|---|---|---|---|---|---|
| Scheduled Learning And Teaching Activities | Lecture | 12 | 1:00 | 12:00 | N/A |
| Guided Independent Study | Assessment preparation and completion | 8 | 1:00 | 8:00 | Drop-in sessions |
| Guided Independent Study | Assessment preparation and completion | 1 | 26:00 | 26:00 | Revision for final examination |
| Guided Independent Study | Assessment preparation and completion | 1 | 2:00 | 2:00 | Final examination |
| Scheduled Learning And Teaching Activities | Practical | 6 | 2:00 | 12:00 | Dry Labs |
| Scheduled Learning And Teaching Activities | Workshops | 3 | 1:00 | 3:00 | Workshop for each thematic block |
| Guided Independent Study | Independent study | 1 | 16:00 | 16:00 | Skills practice |
| Guided Independent Study | Independent study | 1 | 21:00 | 21:00 | Background reading and practice examination questions |
| Total | 100:00 |
Teaching Rationale And Relationship
N/A
Assessment Methods
The format of resits will be determined by the Board of Examiners
Exams
| Description | Length | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|---|
| Written Examination | 120 | 2 | A | 100 | N/A |
Formative Assessments
| Description | Semester | When Set | Comment |
|---|---|---|---|
| Report | 2 | M | Formative Assessment (practical skills) |
Assessment Rationale And Relationship
The examination/final assessment will test the student’s knowledge and understanding of the work content as well as the problem-solving skills. The practical formative assessment will test practical skills. The in course assessment will test information literacy and presentation skills.
Reading Lists
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- CHY8830's Timetable