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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:
*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 a minute familiarizing yourselves with:

e) Read this:

f) Download this PDB file (.gz):


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

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  • John S.

    Very interesting topic and tools. Still digesting it all

    June 19, 2013

  • Connor D.


    June 19, 2013

  • Anitha B.

    Is this going to happen in the lab...will we need to wear closed toe shoes?

    June 17, 2013

    • Raymond M.

      This is a computer course, so no lab work. Closed toed shoes are not a requirement, just a suggestion, for lab work

      June 18, 2013

  • kristen

    Anyone else here from San Francisco who would be interested in carpooling?

    June 12, 2013

  • Patrik

    Cool! By the way, I just found out that Chimera is one of the best ways to go straight from a protein structure in PDB to an STL file that can be printed on our new 3D printer! I want to see if I can print this one:

    June 10, 2013

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