Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits. Why not let us know how they compare to the tools that you use in the comment threads?
This is cross-posted on Soapbox Science.
My favorite thing about all the online science apps and tools is that they make real science accessible to anyone – even sixth graders. Last fall, I taught a course through Citizen Schools, an after school program for middle schoolers. Part of the program includes what is called “apprenticeships”, in which people come in and teach something about their job or profession. As a scientist, I decided I wanted to teach the kids about structure-based drug design.
The goal of the class was to teach the kids a little bit about what proteins look like and how they can use that knowledge to design drugs. I wanted to show students that they can do real scientific research, similar to what scientists are doing now. Using HIV-1 protease as our model system, we used the program Pymol to visualize the protein bound to different HIV drugs and decided on what types of changes we could make to those drugs to hopefully make them bind better.
Next, the kids went into the computer lab and drew their new drugs in MarvinSketch (a great, intuitive, easy-to-use chem drawing software). There are a lot of great chem drawing programs out there, but I chose MarvinSketch because it’s free, it’s easy to use, and it has some fun features. The kids got a kick out of using the molecular dynamics feature and seeing their molecules wiggle and dance.
After drawing their drugs, we docked the molecules onto the HIV-1 protease structure using the Autodock/Vina plugin for Pymol. I spent a lot of time looking for a docking software that I thought sixth graders could use, and I picked Autodock/Vina because it’s easy to use, has a decent GUI interface, and works with Pymol, which I already knew how to use. With Autodock/Vina, you take a PDB structure of a protein and a PDB structure of a small molecule, define a binding site, and the program determines and ranks the top ten conformations of the molecule docked onto the protein.
Drug bound to HIV-1 protease (designed by sixth grade student)
The overall goal was to have students look at how current drugs interact with HIV-1 protease, generate hypotheses on how to change the drugs to make them better and then make those drugs with the computer and see if they bind. All the while, the students would be using tools and programs that real scientists use in the lab.
So, did it work? I knew going in that I had my work cut out for me. The concepts of atoms and molecules are so abstract and esoteric that it’s hard to conceptualize them, but using the tools above really helped the kids visualize these things. I know there was some disconnect on what molecules actually are, like how big they are, where they’re found, how they are a part of living things but not themselves living. Also, because we didn’t go into depth about things like salt bridges, hydrogen bonds, and hydrophobic interactions, the “design” part of the structure-based drug design was a little more random than rational.
But for me, the most important lesson that every student walked away with was that they could be scientists and that they could actually help solve the problems of the world.
While I thought that my approach to teach structure-based drug design was kind of clever, it seems that an upcoming version of Fold-it may do something similar, all in one program.
You can follow the online conversation on Twitter with the #ToolTales hashtag and you can read Mary Mangan’s Tool Tale here, Dr Peter Etchells’s Tool Tale here, Alan Cann’s here, Jerry Sheehan’s here, Boris Adryan’s here, Anthony Salvagno’s here, Daniel Burgarth and Matt Leifer’s here, Zen Faulkes’s here, Mike Biocchi’s here, Susanna Speier’s here, Derek Hennen’s here, Musa Akbari’s here, Benedict Noel’s here, Chris Surridge’s here and Gerd Moe-Behrens’s here.
