Lecture: 3 hours

Discussion: 1 hour

Prerequisite: Graduate standing

Grading: Letter; homework (50%) final project (50%)

Catalog Description:

Algorithmic problems in structural biology; protein structure classification; protein structure prediction (including comparative modeling and ab initio protein structure prediction); molecular simulations (molecular dynamics and Monte Carlo simulations).

Expanded Course Description:

  1. Introduction to Protein Structure
  2. Protein Structure Classification
    1. Identification of protein domains
    2. Protein structure superposition
    3. Classifications
  3. Energy Functions
    1. Semi-empirical energy functions
    2. Solvation
    3. Statistical potentials
  4. Comparative Modeling
  5. Ab initio Protein Structure Prediction
  6. Biogeometry
  7. Molecular Simulations
  8. Protein Design
  9. Databases and Web Services


Typically, the final project will be a decoy protein structure prediction problem. It will be based on many resources available on the web.


Selected review papers and technical papers and class notes will be used.


The function of a protein is directly related to its three-dimensional structure, which in turn is defined by its sequence; unraveling the underlying codes is currently the subject of considerable research. These efforts are interdisciplinary, and involve physics, chemistry, mathematics, computer science and molecular structural biology. The goal is to provide enough background in these different disciplines, with a strong emphasis on their computational aspects, such that students can start using protein structure modeling in their work and ultimately can pursue research in this area.

Instructor: P. Koehl

Prepared by: P. Koehl (January 25, 2006)

Overlap Statement:

ECS 229 covers advanced research topics in computational structural biology, focusing on protein structure modeling. Students are exposed to the latest developments in computer science as well as in physics, mathematics and biology that apply to computational biology. As such, ECS 229 has a minor overlap with PHY 210, which covers analytic techniques to solve differential equations, including those involved in the calculation of the energetics of proteins.