[MM] Molecular Modelling

[MM] Molecular Modelling

This module will provide an introduction to the theory and practice of computer-based molecular modelling techniques such as molecular mechanics and dynamics, homology modeling and molecular docking that are becoming increasingly important to the practice of Structural Biology.


Dr Arvind Varsani (Electron Microscope Unit) has a Pharmaceutical Chemistry and Molecular Biology background. He will present lectures on various aspects of virus structures, assist in the electron microscopy module and provide molecular biology support for the programme. Dr Muhammed Sayed, Department of Biotechnology (UWC), is a protein crystallographer who completed his post-doctoral studies under Professor Tom Blundell at Cambridge University. He will supervise the web-courses in protein structure and protein crystallography. His goal is to develop protein crystallography as a practical discipline. Lecturers also include Kevin Naidoo, Michelle Kuttel and Colin Kenyon.

Main Outcomes

The ability to:

  • understand the principles of molecular modeling and homology modelling,
  • use appropriate software to perform optimizations of molecular structures, run molecular dynamics calculations, perform normal mode analysis, create a homologous structure model from a know structure and perform molecular docking calculations.

This module descriptor document also can be downloaded as an MS-Word document.

Main Content

  • Molecular Mechanics
  • Molecular Dynamics
  • Structure based sequence alignment
  • Homology modeling
  • Molecular docking
Home Department: Computer Science (UCT)
Module description (Header): Computational and Mathematical Primer
Generic module name: Structural Biology
Alpha-numeric code: STB705
Credit Value: 15 Credits
Duration: 6 Weeks
Module Type: P
Level: 8
Co-requisites: None
Prohibited combinations: None
Learning time breakdown (hours):
Contact with lecturer/tutor: 60
Assignments & tasks: 40
Tests & examinations: 5
Practicals: 0
Selfstudy: 35
Total Learning Time 150
Methods of Student Assessment: Weekly computer based tutorials will count approximately equally towards the final mark. Students will be required to make an oral presentation. Moderation will be internal.


Online Lectures

Michelle Kuttel

Kevin Naidoo

Arvind Varsani


Baker, TS and JE Johnson. 1996. "Low resolution meets high: towards a resolution continuum from cells to atoms." Current Opinion in Structural Biology, 6 (5): 585-594.

Bourne, PE and H Weissig. 2005. Structural Bioinformatics. Hoboken, NJ, USA: John Wiley & Sons, Inc., Methods of Biochemical Analysis, Vol 44, 1st ed.

Chacon, P and W Wriggers. 2002. "Multi-resolution contour-based fitting of macromolecular structures." Journal of Molecular Biology, 317 (3): 375-384.

Chacon, P, F Tama, and W Wriggers. 2003. "Mega-dalton biomolecular motion captured from electron microscopy reconstructions." Journal of Molecular Biology, 326 (2): 485-492.

Hoenger, A, S Sack, M Thormahlen, A Marx, J Muller, H Gross, and E Mandelkow. 1998. "Image reconstructions of microtubules decorated with monomeric and dimeric kinesins: comparison with x-ray structure and implications for motility." Journal of Cell Biology, 141 (2): 419-430.

Leach, AR. 2001. Molecular Modelling: Principles and Applications. Harlow, England: Prentice Hall, 2nd ed.

Rayment, I, HM Holden, M Whittaker, CB Yohn, M Lorenz, KC Holmes, and RA Milligan. 1993. "Structure of the actin-myosin complex and its implications for muscle contraction." Science, 261 (5117): 58-65.

Rossmann, MG. 2000. "Fitting atomic models into electron-microscopy maps." Acta Crystallographica Section D Biological Crystallography, 56 (10): 1341-1349.

Smith, TJ, NH Olson, RH Cheng, H Liu, ES Chase, WM Lee, DM Leippe, AG Mosser, RR Rueckert, and TS Baker. 1993. "Structure of human rhinovirus complexed with Fab fragments from a neutralizing antibody." Journal of Virology, 67 (3): 1148-1158.

Spahn, CM, JS Kieft, RA Grassucci, PA Penczek, K Zhou, JA Doudna, and J Frank. 2001. "Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit." Science, 291 (5510): 1959-1962.

Tama, F, W Wriggers, and CL Brooks. 2002. "Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory." Journal of Molecular Biology, 321 (2): 297-305.

Tama, F, O Miyashita, and CL Brooks. 2004. "Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis." Journal of Molecular Biology, 337 (4): 985-999.

Volkmann, N and D Hanein. 1999. "Quantitative fitting of atomic models into observed densities derived by electron microscopy." Journal of Structural Biology, 125 (2-3): 176-184.

Volkmann, N, D DeRosier, P Matsudaira, and D Hanein. 2001. "An atomic model of actin filaments cross-linked by fimbrin and its implications for bundle assembly and function." The Journal of Cell Biology, 153 (5): 947-956.

Wriggers, W, R Milligan, and J McCammon. 1999. "Situs: A package for docking crystal structures into low-resolution maps from electron microscopy." Journal of Structural Biology, 125 (2-3): 185-195.

Wriggers, W and S Birmanns. 2001. "Using situs for flexible and rigid-body fitting of multiresolution single-molecule data." Journal of Structural Biology, 133 (2-3): 193-202.

Wu, Xiongwu, Jacqueline Milne, Mario Borgnia, Alexey Rostapshov, Sriram Subramaniam, and Bernard Brooks. 2003. "A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy." Journal of Structural Biology, 141 (1): 63-76.