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:
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).
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: http://pymol.org/educational/
*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: http://avogadro.openmolecules.net/wiki/Main_Page
c) Chimera: http://www.cgl.ucsf.edu/chimera/
d) Spend 1 minute familiarizing yourselves with: http://www.rcsb.org/pdb/home/home.do
e) Read this: http://www.rcsb.org/pdb/101/motm.do?momID=77&evtc=Suggest&evta=Moleculeof%20the%20Month&evtl=OtherOptions
f) Download this PDB file (.gz): http://www.rcsb.org/pdb/explore/explore.do?structureId=1GAL