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Held: Tuesday, 25 October 2011
We begin to consider computational approaches to predicting the structure
- Reading: Chapter 7.
- Due: Set up second PCR on Wednesday!.
- RIP John McCarthy, inventor of LISP.
- We're playing with the schedule a bit. The following deadlines are subject to revision.
- Due November 1: Web Exploration from Chapter 7. (Further details forthcoming.)
- Due November 3: Programming Exploration from Chapter 7. (Further details forthcoming.)
- Due November 8: Response to Krings et al. (Distributed Thursday.)
- Due November 10: Project Proposals. (Further details forthcoming.)
- We plan to return outstanding work next week.
- Don't forget that we have lots of lab this week and next. (In particular, Thursday and next Tuesday are going to be long classes.)
- If you have not read Chapter 7 yet, you should read it asap.
- EC for any of the Grinnell College Young Innovator for Social Justice events (Awards ceremony Tuesday night; Coffee break on Wednesday at 2:30; Symposium on Wednesday at 4:15; Symposium Wednesday at 8:00 p.m.; Morris Dees Convo).
- EC for Wednesday's noontime Biology Seminar, Stuart Allison from Knox on "Ecological restoration and environmental change - a geographic comparison of attitudes towards restoration and the practice of restoration.".
- EC for Wednesday's afternoon Biology Seminar at 4:15 on "One year Master's programmes in Environmental & Life Sciences at the only 100% graduate university in England" and "'Environmental Futures' A Summer program designed for students completing their junior year at Midstates Math & Science Consortium Colleges."
- EC for Fridays's Biology Seminar.
- No EC for this week's Thursday extra (Discrete Structures and Math Requirements in CS).
- Next Tuesday at noon: Study abroad options in Budapest in CS.
- Protein structure: What is it and why care?
- The Chou-Fasman Algorithm.
- Wet Lab.
- 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
- 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
- Take proteins with known structure
- For each amino acid, count
- Total number of appearances
- Appearances in alpha helices
- Appearances in the interior of alpha helicies
- Appearances in beta sheets
- Appearances in beta turns (postions 0, 1, 2, 3)
- Total each column
- For each amino acid, find the frequency
- 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
- We then apply a second heuristic to the expanded sequence