Computational Techniques in Structural Bioinformatics


CS483/CS683    Winter 2015    




Forbes Burkowski




Assignments Winter 2015:


Assignment #1

Assignment #2

Assignment #3

Assignment #4

Assignment #5 Due date: Thurs. Apr. 2 Delaunay Starter Script


Project Requirements



Some notes related to Assignment #1:  Getting Started with Chimera and Python


Office Hours Information


The magic that is life ultimately takes place on the surfaces of biomolecules.  Biochemical interactions at the active site of a protein surface are involved in both the normal reactions that support life processes and the contrived reactions that constitute therapeutic intervention via drugs.  In both situations, the biochemist and the bioinformatician must take on the challenge of working with large collections of high dimensional data dealing with three-dimensional structures.


The main emphasis of the course will be the application of computational approaches to problems in structural bioinformatics.  This includes algorithms for database storage and retrieval of biomolecular structures and the geometric algorithms that help us analyze and model both macromolecular chains and the surfaces that they form. 



Computational and Visualization Techniques for Structural Bioinformatics Using Chimera


Author:  Forbes Burkowski


Website for the text:


Some additional reference texts will be mentioned in the first set of slides.

Copies of all transparencies used in class will be made available:


Course Notes




•        There will be five assignments corresponding to various major topics of the course. 


–      Marking scheme CS483.    Assignments 30%,   Midterm 30%,   Project 40%.


–       Marking scheme CS683    Any 4 of the 5 Assignments: 25%,   Midterm: 25%,  Project: 50%. 

•        The project will include a 30 minute class presentation.

•        You must first submit a project proposal for approval and constructive criticism prior to the end of February.  This proposal will be part of Assignment 3.

–       Note: To pass CS483/683, the weighted average of the Midterm and Project must be more than 50%.
If this average is below 50%, then that average becomes the final grade (project or assignments are not included in the final grade).




Academic Honesty


The usual penalties for academic dishonesty will apply: -100% on an assignment if there is evidence of copying or plagiarism.


So that there are no future misunderstandings, please read the following:


In any program you write, each line of code should come from your effort only.


If you are writing text that is part of the assignment, each sentence that you write will fall into one of the following categories:


1.    The sentence is expressed in your own words and expresses your own ideas.

2.    The sentence is expressed in your own words but the ideas or concepts are from somebody else.

In this case you must supply a reference at the end of your document and a pointer to that reference must be associated with that sentence (for example, the pointer is either within the sentence or immediately after the paragraph if the entire paragraph contains your sentences but are describing someone else’s ideas.

3.    The sentence is copied from work done by somebody else.

In this case you must use indentation and quotation marks to clearly specify the limits of the copied material.  You must then provide a pointer to a reference as described in the previous point.