# Class 18: Structure Prediction (1)

Back to Mid-Semester Examination. On to Structure Prediction (2).

This outline is also available in PDF.

Held: Tuesday, 3 November 2009

Summary: We begin to consider computational approaches to predicting the structure of proteins.

Related Pages:

Notes:

• Fun event Saturday a.m.: Grinnell Destination ImagiNation Fun Run/Walk. More info outside my office.
• If you are registered in Powesheik county, don't forget to vote.
• Don't forget Thursday's Thursday Extra: The Ontological domain model of medical imaging informatics. (Yes, it will be more interesting than it sounds.)

Overview:

• Protein structure: What is it and why care?
• The Chou-Fasman Algorithm
• Web exploration

## Structure Prediction

• Lots of kinds of structures:
• Primary, secondary, tertiary, quartenary
• Proteins have structure.
• RNA has structure.
• Even DNA sometimes has non-obvious structure
• Why do we care?
• Can we write programs that predict structures?
• Not perfectly (at least not yet)
• But can get some potentially useful info

## The Chou-Fasman Algorithm

• Chou and Fasman provided an algorithm (well, perhaps more of a heuristic) for predicting some secondary structure:
• alpha helices
• beta sheets (aka beta strands)
• hairpin turns (aka beta turns)
• The algorithm is mostly statistical
• We look at the likelihood that each amino acid participates in each structure
• Basic algorithm: We pass a sliding window along the sequence
• The window selects a small number of amino acids (e.g., six)
• When some heuristic is met (e.g., at least four amino acids out of six have a high probability of participating in an alpha helix), we expand out
• We then apply a second heuristic to the expanded sequence

## Web Exploration

Back to Mid-Semester Examination. On to Structure Prediction (2).

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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Samuel A. Rebelsky, rebelsky@grinnell.edu

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