ECS 229: Advanced Computational Structural Bioinformatics

ECS 229
Advanced Computational Structural Bioinformatics
Effective Term
2016 Spring Quarter
Learning Activities
Lecture - 3.0 hours
Discussion - 1.0 hours
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).
Graduate standing.
Enrollment Restrictions
Pass One and Pass Two open to Graduate Students in Computer Science only.

Summary of Course Content
I. Introduction to Protein Structure

II. Protein Structure Classification
A. Identification of protein domains
B. Protein structure superposition
C. Classifications

III. Energy Functions
A. Semi-empirical energy functions
B. Solvation
C. Statistical potentials

IV. Comparative Modeling

V. Ab initio Protein Structure Prediction

VI. Biogeometry

VII. Molecular Simulations

VIII. Protein Design

IX. Databases and Web Services

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

Potential Course Overlap
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.

Course Category