CAP5515: Computational Molecular Biology
Term: Spring 2005
Time: Tuesday 8:30am-10:25am, Thursday 9:35am-10:25am
Location: CSE 222
Office hours: Tuesday 10:25am-11:25am, Thursday 10:25am-11:25am
Professor: Alper Üngör
Computational Biology is the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. This course will survey the fundamental concepts in computational molecular biology, including

  • Protein Modeling
  • Alpha Shapes
  • Molecular & Skin Surfaces
  • Protein Docking
  • Scoring Functions
  • Interfaces & Interactions
  • Protein Folding
  • Structure Predition
  • Protein Data Bank
  • Drug Design
  • Molecular Visualization
  • Structure Determination
  • X-ray Crystallography
  • NMR Spectroscopy

    • Credits: 3
    Pre-requisites: COP 3530 or equivalent, or Instructor's permission
    Textbooks (Recommended):
  • Molecular Modeling: Basic Principles and Applications, 2nd Edition, Hans-Dieter Höltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers, September 2003
  • Structural Bioinformatics, Philip E. Bourne, Helge Weissig, 2002. Wiley-Liss.
  • Introduction to Protein Structure, Carl Branden, John Tooze Garland Publishing, 2nd Edition, January 1999.
  • Molecular Modelling: Principles and Applications, 2nd edition, Andrew R. Leach, Published by Pearson Education EMA, January 2001.
  • I will also distribute survey and research papers from recent conferences and journals on the course web site.
    • Coursework: Grades will be based on homeworks (30%), presentations and participation (20%), and a semester project (50%).
    Alper Üngör (ungor@cise.ufl.edu) December 2004