Postgraduate

Modules

Modules

CHY8830 : Molecular Simulations and Computer-aided Drug Design (CADD)

Semesters
Semester 2 Credit Value: 10
ECTS Credits: 5.0

Aims

The purpose of this course is to equip students with solid foundations in structure-based drug design, providing them with an overview on modern methods in molecular simulations used in computational drug discovery. This will be organised in two thematic blocks.

The first block will cover some key techniques used in molecular simulations of drug-protein complexes, target identification and validation and in structure-based ligand design. These will include molecular mechanics, molecular dynamics (MD) simulations, and molecular docking calculations. The fundamental ideas behind the molecular force fields and their applications will be accompanied by some case studies.

The second thematic block will cover some more advanced molecular simulation methods, elements of thermodynamics and statistical mechanics, and modern quantum mechanics calculations. 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

Molecular docking, molecular mechanics, and molecular dynamics (MD) simulations
Dr. Agnieszka K. Bronowska

Fundamental concepts in molecular mechanics: force fields, molecular dynamics and applications. Molecular docking and virtual screening. Case studies in computer-aided drug design.


Fundamental QM ideas and advanced molecular simulation methods in CADD
Dr. Daniel Cole

Key concepts and applications of quantum mechanics (QM). Monte Carlo methods, thermodynamics and free energy methods. Case studies in computer-aided drug design.

Teaching Methods

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

Teaching Activities
Category Activity Number Length Student Hours Comment
Scheduled Learning And Teaching ActivitiesLecture121:0012:00N/A
Guided Independent StudyAssessment preparation and completion12:002:00Final examination
Guided Independent StudyAssessment preparation and completion112:0012:00Revision for final examination
Guided Independent StudyAssessment preparation and completion54:0020:00Writing up lab reports
Scheduled Learning And Teaching ActivitiesPractical62:0012:00Dry Labs
Scheduled Learning And Teaching ActivitiesWorkshops41:004:00Workshop for each thematic block
Guided Independent StudyIndependent study123:0023:00Background reading and practice examination questions
Guided Independent StudyIndependent study115:0015:00Skills practice
Total100:00
Teaching Rationale And Relationship

N/A

Assessment Methods

Please note that module leaders are reviewing the module teaching and assessment methods for Semester 2 modules, in light of the Covid-19 restrictions. There may also be a few further changes to Semester 1 modules. Final information will be available by the end of August 2020 in for Semester 1 modules and the end of October 2020 for Semester 2 modules.

The format of resits will be determined by the Board of Examiners

Exams
Description Length Semester When Set Percentage Comment
Written Examination1202A50N/A
Other Assessment
Description Semester When Set Percentage Comment
Report2M50Dry Lab Reports
Assessment Rationale And Relationship

The examination will test the student’s knowledge and understanding of the work content. The in course assessment will test information literacy and presentation skills.

Reading Lists

Timetable