ECS 129: Computational Structural Bioinformatics

Subject
ECS 129
Title
Computational Structural Bioinformatics
Status
Active
Units
4.0
Effective Term
2019 Winter Quarter
Learning Activities
Lecture - 3.0 hours
Discussion - 1.0 hours
Description
Fundamental biological, chemical and algorithmic models underlying computational structural biology; protein structure and nucleic acids structure; comparison of protein structures; protein structure prediction; molecular simulations; databases and online services in computational structural biology. GE Prior to Fall 2011: SciEng. GE: SE.
Prerequisites
(BIS 002A or MCB 010); (ECS 010 or ECS 032A or ECS 036A)
Enrollment Restrictions
Pass One open to Computer Science, Computer Science Engineering, and Biotechnology majors only.

Summary of Course Content

I. Introduction: Top Challenges in Bioinformatics

II. Bio-molecular Structures

  • 
A. Nucleic acids
  • 
B. Protein

III. Comparing Sequences and Structures

  • 
A. Sequence alignment
  • 
B. Structure alignment

IV. Protein Structure Databases

  • A. Protein domains
  • B. Protein structure classification 

V. Stability of Bio-molecules 


  • A. Semi-empirical energy functions
  • 
B. Statistical potentials 

VI. Structure Prediction 


  • A. Protein: Comparative modeling 

  • B. Protein: Ab initio prediction 

  • C. RNA: secondary structure and tertiary structure predictions 

VII. Bio-molecular Simulations 

VIII. Drug Design 

IX. Databases and Web Services 



Illustrative Reading


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



Potential Course Overlap


ECS 124 (Theory and Practice of Bioinformatics) and ECS 129 are complementary courses with minimal overlap covering bioinformatics. ECS 124 focuses on sequence analysis, while ECS 129 covers the structural challenges in bioinformatics.

Course Category

Upper Division