Bioinformatics III (Structural Bioinformatics)

COM S 569

Offered during Fall Semester each year.

  1. Credits: 3 credit hours
  2. Instructor's or course coordinator's name: Rober L. Jernigan
  3. Textbook, title, author, and year
    • Protein Actions, I. Bahar, R.L. Jernigan, K. Dill, 2017
    • Protein Structure and Function, Petsko, 2004
    • Introduction to Protein Structure, Branden and Tooze, 1998
    • Computational methods for protein structure prediction and modeling (volume 1 and 2), Xu, Xu, and Liang, 2007
    • Lecture Notes on Computational Structural Biology, Zhijun Wu, 2008
    • Molecular Modeling and Simulation, Tamar Schlick, 2002
    • Structural Bioinformatics, 2nd Edition, Jenny Gu and Philip Bourne, 2009
    • Protein Structure Prediction: a practical; approach, M. Sternberg, 1996
    • Textbook of Structural Biology, Liljas et all, 2010
    • Molecular Biophysics, Michael Daune, 1999
    • Introduction to Proteins: Structure, Function, and Motion, Kessel et al, 2010
    • Understanding Bioinformatics, M. Zvelebil, J. Baum, 2007
  4. Other supplemental materials: None

Course Information

  1. Brief description of the content of the course: Molecular structures including genes and gene products: protein, DNA, and RNA structure. Structure determination methods, structural refinement, structure representation, comparison of structures, visualization, and modeling. Molecular and cellular structure from imaging. Analysis and prediction of protein secondary, tertiary, and higher-order structure, disorder, protein-protein, and protein-nucleic acid interactions, protein localization and function, bridging between molecular and cellular structures. Molecular evolution.
  2. Prerequisites or co-requisites: BCB 567, BBMB 316, GEN 409, STAT 430

Course Outcomes

  1. Established an essential foundation of structural informatics
  2. Computationally manipulated and analyze molecular structures
  3. Become familiar with the frontier of current research
  4. Gained research experience


  1. Protein Structure basics
  2. PDB formal
  3. Visualization and Graphics
  4. Empirical Force fields
  5. Knowledge-based Energy functions
  6. Nucleic Acid Structures
  7. Molecule Machines
  8. X-ray Crystallography
  9. NMR
  10. Protein geometry
  11. Identification of domains
  12. Protein structure comparisons
  13. Classification of protein folds
  14. Sequence analysis
  15. Local structure prediction
  16. Homology Modeling
  17. Threading
  18. Ab initio protein structure prediction
  19. Protein-protein and protein-nucleic acid interactions
  20. Molecular dynamics
  21. Other sampling methods
  22. Coarse-grained models
  23. Mechanisms and regulation
  24. Protein design and drug selection