Molecular Modelling and Database Mining (P01563)

? Credit Points : 10 ? SCQF Level : 11 ? Acronym : BIO-P-MOLMOD

This module will expose the student to the computational methods involved in structure-based drug design. The student will work on a small project carry out the different steps with a high degree of independence. Supervision will be provided on an introductory basis as well as ad hoc.

Entry Requirements

? Pre-requisites : Entry to the course will be for students already holding (or expecting to hold) an Honours degree or equivalent in a biological subject such as biochemistry, molecular biology, biophysics, pharmacology. Students with a background in chemistry, physics, computer science or informatics will also be considered and those with other scientific or medical backgrounds should contact the Course Director.

? Costs : None

Subject Areas

Home subject area

Postgraduate, (School of Biological Sciences, Schedule K)

Delivery Information

? Normal year taken : Postgraduate

? Delivery Period : Semester 1 (Blocks 1-2)

? Contact Teaching Time : 2 hour(s) per week for 10 weeks

Summary of Intended Learning Outcomes

Overall: a working knowledge of the software and approaches in current use for protein modelling and structure-based drug design.

Specifically:
1. BLAST, AA alignment, PDB, PFAM,
Given a protein aa sequence, search for homologous proteins. Identify available crystal structures. Secondary structure prediction.
2. Homology modelling
Generate a homology model using suitable software (Modeller, etc).
3. Database mining with LIDAEUS
Search for suitable compounds to bind in the active site by means of virtual screening.