Module Code - Title:
PH6021
-
PREDICTIVE BIOMOLECULAR MODELLING TOOLS
Year Last Offered:
2025/6
Hours Per Week:
Grading Type:
N
Prerequisite Modules:
Rationale and Purpose of the Module:
This module will introduce the students to the computational physics, chemistry and biology underpinning the latest breakthroughs in disease treatment and regenerative medicine. With a particular focus on drug-protein, protein-protein, and protein-surface interactions, students will gain a molecular level understanding of how to re-engineer advanced molecular biology processes including genetic code translation, neurodegenerative disease progression, and cell growth on tissue engineering scaffolds. The required high-performance computing hardware, molecular modelling software, and data analytics tools will be demonstrated and discussed through interactive online tutorials.
Syllabus:
Predictive modelling of biological materials, from genomics to proteomics to molecular structures - amino acids, peptides, proteins, antibodies, nucelotides and sugars. Nanoscale physics underlying molecular interactions: Electrostatic interactions, Solvation, van der Waals interactions, Surface interactions, Re-engineering biomolecular structures. Predictive modelling of novel nanomedicines: Expanding the genetic code, Blocking aggregation of neurotoxic proteins, Sculpting anti-cancer drugs. Student online presentations on topics such as modelling ion trafficking through transmembrane proteins, molecular-level engineering of sugar-siRNA complexes as gene delivery vector, and preserving antibody structures using computationally designed excipients.
Learning Outcomes:
Cognitive (Knowledge, Understanding, Application, Analysis, Evaluation, Synthesis)
On successful completion of this module, students will:
1) Be able to describe the molecular scale physics underlying interactions between biomolecules
2) Be able to explain how computer simulations can help to quantify and predict the assemblies that biomolecules will form in solution and on surfaces
3) Be able to describe examples of how molecular scale re-engineering can aid development of nanomedicines
4) Be able to research and discuss topics in the current literature on nanomedicine
Affective (Attitudes and Values)
On successful completion of this module, students will:
1) Demonstrate appreciation of the relative strengths of non-covalent and covalent forces in driving biomolecule conformation and interactions
2) Be able to discuss the relative merits of different molecular-level strategies to deliver drugs inside cells
3) Be able to justify usage of different techniques to predict biomolecule structure and function in complex multi-biomolecule assemblies in solution and on biological scaffolds
4) Be able to discuss the coding development behind modelling software
Psychomotor (Physical Skills)
On successful completion of this module, students will:
Perform computer simulations of docking small molecular drugs to proteins
How the Module will be Taught and what will be the Learning Experiences of the Students:
How the Module will be Taught and what will be the Learning Experiences of the Students:
The module will be taught from a theoretical perspective with formal lectures and tutorial sessions. The online modelling component will develop key skills in computer simulations, which reinforce the lecture content. Practicals will be undertaken online in molecular dynamics based computer modelling.
Research Findings Incorporated in to the Syllabus (If Relevant):
Applications from research findings that are current will be used to reinforce the importance of particular programmatic aspects. For example protein re-engineering to expand the genetic code will be highlighted.
Research Findings Incorporated in to the Syllabus (If Relevant):
Prime Texts:
Banaszak, Leonard. (2000)
Foundations of structural biology.
, San Diego, Calif. : Academic Press
Leach, Andrew R. (1996)
Molecular Modelling Principles and Applications.
, Harlow : Longman
Other Relevant Texts:
Programme(s) in which this Module is Offered:
Semester(s) Module is Offered:
Autumn
Module Leader:
shayon.bhattacharya@ul.ie