Curriculum & Course Descriptions

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BS3008 Computational Biology & Modelling

Course Coordinator: Associate Professor MU Yuguang (email: YGMu@ntu.edu.sg)

Academic Unit: 3 AU

Availability: Semester 2

Pre-requisite: None

Course Type: BS-Major-PE, BMS-Major-PE

Language of instruction: English

Teaching hours:  Lectures: 26 hours; Tutorials: 9 hours; Practicals: 9 hours

Learning Objective: This course presents both the physical foundations of biomolecular dynamics simulation methods and practical training in use of these methods. The concepts of physiochemical properties of molecules, structure-energy relationship, dynamical point of view of protein/DNA structures, are introduced. Emphasis will be on how these computational tools are applied to biological areas such as protein folding, membrane fusion, enzyme activity, drug-target interaction. These methods are illustrated with modern computer based laboratory practicals with graphical display of biological molecules.

Content: Topics covered will be a variety of computational methods and modelling strategies, such as classical force field based on quantum theory and coarse grained models. Basic sampling techniques, such as Monte Carlo, molecular dynamics and Langevin dynamics simulation will be described.  Principles in structure-based drug design, such as docking, scoring, large scale ligand database screening, are also demonstrated.

Learning Outcome:

  • Understand physical principles of molecular modelling: science and art
  • Be familiar with large-scale computing platform
  • Set up simple modelling study with suitable physical models
  • Build data analysis ability
  • Appreciate modelling as an important complimentary tool in biological research

Textbooks/References

  • Schlick, Tamar (2002)  Molecular Modeling: An Interdisciplinary Guide (Springer-Verlag).
  • Hans- Dieter Hoeltje, et al.(2003)  Molecular modeling: Basic Principles and applications, 2rd Edition (WILEY-VCH Verlag)