Molecular Modeling & BioPioneering: Idea, Simulation, Planning

Engineering proteins and biochemical systems has been greatly improved and accelerated in the last decade due to the accessibility of molecular modelling software. This workshop will take you into the molecular world and show you how to use free open source software to view and manipulate proteins and make beautiful images.

Whether you're new to the life sciences or have years of experience, this workshop will show you how to start a bioengineering project, introduce you to the realm of bio-possibility, and show you tools needed to test some of your hypotheses in silico long before you need a lab bench or while you hone your wet-lab skills at one of BioCurious' many great wet-lab workshops.

You will be taught how to explore online databases where protein data is stored, manipulate proteins using molecular modelling software, and render beautiful images of those proteins so that you can effectively communicate your work. Although it may sound daunting, this class is for all ages! We will cover a plethora of topics including DNA, protein, protein engineering, biochemistry, molecular dynamics, and more!

Those signed up will require more info before hand (will also be distributed prior to the workshop)

What is molecular Modelling?

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.

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 a 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

Biography:

Justin Pahara has more than a decade of bioengineering experience as well as extensive knowledge of synthetic biology. Justin is passionate about biology as a technology and believes that with just a little more tinkering, many of humanities greatest challenges can be overcome using biology. Justin earned his Ph.D. from the Department of Chemical Engineering and Biotechnology at the University of Cambridge, earned his B.Sc. and M.Sc. at the University of Alberta in Immunology and Infection and Cell Biology, respectively, and is a graduate from Singularity University.

© Justin Pahara 2013