ECS129: Computational Structural Bioinformatics
Winter 2016
Patrice Koehl (koehl@cs.ucdavis.edu)
Information sheet
Class Web page: http://www.cs.ucdavis.edu/~koehl/Teaching/ECS129/index.html
Check here for announcements, handouts (pdf and ppt), recommended readings, quizzes,
assignments, etc.
Lectures: MWF 9:00 – 9:50 am, 147 Ohlson
Discussion: Th 5:10 – 6:00 pm , 205 Ohlson
Office hours: Thu 14:00 – 16:00 Kemper Hall, Room 3059; also by appointment (send
me an e-mail)
Contacts: koehl@cs.ucdavis.edu
I answer to ALL e-mails. I do NOT guarantee however that I answer PROMPTLY…
Attendance:
- You are expected to attend lectures, and you are responsible for the material
discussed in class.
- Discussions are optional. I will be there, to discuss class materials and papers.
Exams:
There will be one mid-term project. The final will be an exam.
Grading: 50% midterm, 50% final.
Course Description:
I.
II.
III.
IV.
V.
Introduction: top challenges in Bioinformatics
Bio-molecular structures
- Nucleic acids
- Proteins
Comparing sequences and structures
- Sequence alignment
- Structure alignment
Protein Structure databases
- Protein domains
- Protein structure classification
Stability of bio-molecules
- Semi-empirical energy functions
- Statistical potentials
VI.
VII.
VIII.
IX.
Protein structure prediction
- Comparative modeling
- Ab initio prediction
Bio-molecular simulations
Drug design
Databases and web services