Computer Science @ UC Davis | Course Descriptions

ECS 129 COMPUTATIONAL STRUCTURAL BIOINFORMATICS (4) I

Lecture: 3 hours

Discussion: 1 hour

Prerequisite: College level programming course; Biological Science 1A or Molecular and Cellular Biology 10

Grading: Letter; assignments (30%), quizzes (30%), final (40%)

Catalog 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.

Expanded Course Description:

Introduction: Top Challenges in Bioinformatics
Bio-molecular Structures
1. Nucleic acids
2. Protein
Comparing Sequences and Structures
1. Sequence alignment
2. Structure alignment
Protein Structure Databases
1. Protein domains
2. Protein structure classification
Stability of Bio-molecules

Semi-empirical energy functions
Statistical potentials

Bio-molecular Simulations
Drug Design
Databases and Web Services

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

ABET Category Content::
Engineering Science: 1 unit
Engineering Design: 0 unit

Goals:
Students will:

understand the challenges currently faced by structural bioinformatics
be able to understand and efficiently use the tools currently available in this field
develop an interest to pursue research in bioinformatics

Program Educational Outcomes

The ability to work independently
The ability to effectively express ideas through written communication
The ability to construct appropriate abstractions to manage complexity and to think creatively about new problems
The ability to understand the professional ethics and responsibilities of an engineer
The ability to understand the implications of contemporary computing and information processing issues relative to society
The ability to acquire the foundations to be a life-long learner

Instructor: P. Koehl

Prepared by: P. Koehl (November 2005)

Overlap Statement:
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.