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

Semester 2 Credit Value: 10
ECTS Credits: 5.0


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 suitable for large macromolecular systems. 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

• Force fields – the core idea
• Molecular docking and virtual screening
• Interaction energy: scoring functions
• Secondary rescoring
• Hit identification, hit-to-lead conversion, and lead optimisation
• Handling the flexibility in molecular docking
• Case studies 1
• Introduction to molecular mechanics and molecular dynamics
• MM energy minimisation
• Molecular dynamics (MD) simulations
• Analysis
• Handling solvent effects
• Force field development
• MD simulations in non-equilibrium conditions
• Experimental restraints
• When atomistic MM fails
• Coarse-grained simulations
• QM/MM simulations
• Case studies 2

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

• Key concepts of quantum mechanics (QM)
• Methods for solving the Schrödinger equation
• Practical considerations when performing QM calculations
• Electrostatic potential
• Atomic charges
• Intermolecular bonding
• Modelling chemical reactions
• Monte Carlo methods
• Thermodynamics
• Statistical mechanics
• Free energy methods
• Case Studies 3

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
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 ActivitiesLecture121:0012:00N/A
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
Teaching Rationale And Relationship


Assessment Methods

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

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