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Chapter 3: Proteins & Molecular Modelling

The purpose of this meeting will be to talk about Chapter 3 of the Molecular Biology of the Cell textbook that we've been studying. Chapter 3 is about proteins, with a large section on their activity as enzymes. Justin Pahara is planning to show us some related molecular modeling stuff as our activity for the night, here's a snip-it from him:

Hello Everyone!
For our next DIYBIO meet up, I would be excited if the group would allow me to spend a little time sharing my experience with molecular modelling and visualization of protein crystal data using software. It has taken me years to discover, pull together, and understand which software is good for particular activities and I would like to condense this into a short interactive session. We might also have a little time to explore the building of simple molecules…

Also, If you happen to have some red-cyan 3D glasses, please bring them along - the more the better! (I apologize as my collection has recently gone missing).

====Background info====
What is molecular Modelling? (Justin's interpretation):
Molecular modelling entails the use of computers and software in concert with real scientific data and theories to understand the energetics of atomic and molecular systems.

Toolkit & Background - What you need to get going:
1) Bring your laptop (+ 3 button mouse if possible, but don't buy one if you don't have one), ideally with the following programs installed (even though they're open-source, some might require academic credentials… we can work around this):
a) PyMOL:
*I take no responsibility if you have to somehow fudge the registration details ;) IMHO, this is for educational purposes though, so its legit
b) Avogadro:
c) Chimera:
d) Spend 1 minute familiarizing yourselves with:
e) Read this:
f) Download this PDB file (.gz):

Best wishes,

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  • Isha D.

    Hey guys, this might be a cool thing for DIYbio to set up:

    January 24, 2013

  • Eric B.

    I've updated the description of this event to show what we'll all be doing! TL;DR: we're doing chapter 3 of Molecular Biology of the Cell (proteins), and Justin will be showing off molecular modeling software. If you're interested in running some of that yourself, click through and read the description of this event again, Justin has provided some cool links and instructions on what to bring to the event to maximize your ability to participate.

    January 20, 2013

    • roberta b.

      yay!!! this is fantastic! I am stuck with a late course on thursdays, but I will try to make it early enough to catch part of the cool stuff. are you guys going to be around after 9?

      January 21, 2013

    • Eric B.

      yeah, at the very least I'll be hanging around afterwards, so you can always just chill with whoever stays here :-)

      January 22, 2013

  • Anshuman S.

    Hi guys! Could you suggest some beginner level books for Biotechnology?

    January 15, 2013

    • Isha D.

      I have some intro textbooks if you'd like to borrow :)

      January 17, 2013

    • Anshuman S.

      I'm not sure. I'm in my second year of undergrad, and just want to learn the what the building blocks are. Thanks Isha, that' ll be awesome! :D

      January 20, 2013

  • Isha D.

    Will the DIYBio meetings always be on Thursdays? I have a regular Thursday[masked]pm commitment...maybe we could switch it up every once in a while?

    January 17, 2013

    • David L.

      Hi: I said Wednesday, I meant Thursday. But, well, I live at Dundas and Jarvis. Where are you?

      January 18, 2013

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