CS 483 Computational Techniques in Structural Bioinformatics
Objectives
This course will cover algorithms and techniques used in the identification and functional characterization of cellular proteins. Structure of proteins will be investigated with an emphasis on binding sites including computational approaches to protein-protein interactions, ligand-proteins interactions, and drug design.
Intended Audience
CS 483 is intended for students in the Bioinformatics plan in fourth year or those with an interest in the application of current techniques in computer science to the study of macromolecular structure and functionality.
Related Courses
Prerequisites: BIOL 365, CS 341, STAT 231/241.
References
Course notes to be provided by the instructor. Optional text: Structural Bioinformatics: An Algorithmic Approach, Forbes Burkowski, Chapman and Hall/CRC, 2008.
Schedule
3 hours of lectures per week. Normally available in Winter.
Outline
Introduction (2 hours)
Review of the fundamentals in structural bioinformatics: Protein structure, DNA and RNA structure, Visualization tools.
Structure Comparison (4 hours)
Structure superposition. Comparison and alignment algorithms.
Structure Assignment (3 hours)
Secondary structure assignment. Structural domains
Protein Structure Classification (3 hours)
Structure comparison (SCOP, The CATH hierarchy).
Protein Functionality (3 hours)
Inferring function from structure. Structural motifs. Electrostatic interactions.
Protein Interactions with Ligands (6 hours)
Docking algorithms. Scoring functions. Protein flexibility.
Computer-aided Drug Design (12 hours)
Overview of the drug design process. Analog-based design (pharmacophores, QSAR). Structure-based design (docking rigid and flexible ligands, de novo design, peptidomimetism). Design of virtual chemical libraries. Computational approaches to high throughput screening and drug selection. ADMET properties.
Structure Prediction (3 hours)
Secondary structure prediction. Tertiary structure prediction: (Homology modeling, threading, Ab initio folding).
