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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
Semester 2 Credit Value: 10
ECTS Credits: 5.0


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 ActivitiesLecture121:0012:00N/A
Guided Independent StudyAssessment preparation and completion81:008:00Drop-in sessions
Guided Independent StudyAssessment preparation and completion126:0026:00Revision for final examination
Guided Independent StudyAssessment preparation and completion12:002:00Final examination
Scheduled Learning And Teaching ActivitiesPractical62:0012:00Dry Labs
Scheduled Learning And Teaching ActivitiesWorkshops31:003:00Workshop for each thematic block
Guided Independent StudyIndependent study116:0016:00Skills practice
Guided Independent StudyIndependent study121:0021:00Background reading and practice examination questions
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 Examination1202A100N/A
Formative Assessments
Description Semester When Set Comment
Report2MFormative 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