Regarding #2, there are some in silico modeling options to look for chemical interactions that you can work on without getting your hands dirty or spending any money.
If you are trying to find/design a compound to cause a specific effect in bacteria, do you know the target? Are you trying to interact with a specific protein? If you have a specific protein target, you can start to use some molecular modeling type software to at least make guesses as to what type of compound will give you the interaction you want. In general, you can't get the atomic resolution of a protein you'd need to design interactions with any type of microscopy. You'd need to use X-ray crystallography or NMR to get that type of resolution, both of which are still out of reach for the DIY biologist. However, if the structure of your protein of interest has already been found (search pdb.org for your protein), then you are in business. Alternatively, if your protein of interest has enough sequence similarity to proteins with known structures, you can build a homology model (e.g. http://swissmodel.expasy.org/).
Once you have a structure model, you can start o try to dock various compounds computationally to try to find a hit. A lot of the software to do this type of modeling is ridiculously expensive. Thankfully, there are some free/open-source options available. Check out http://autodock.scripps.edu/ for one option.
This is one of the basic workflows that large pharmaceutical companies use to find new drug candidates. It works, but they end up investing millions of dollars to make it work. It's important to understand that computational modeling of macromolecules like protein is still very crude, and there is no guarantee that the results are accurate. You might go through a million compounds in the computer to find 100 compounds that look good in the models to find one that performs well in live cells.
If you are trying to find/design a compound to cause a specific effect in bacteria, do you know the target? Are you trying to interact with a specific protein? If you have a specific protein target, you can start to use some molecular modeling type software to at least make guesses as to what type of compound will give you the interaction you want. In general, you can't get the atomic resolution of a protein you'd need to design interactions with any type of microscopy. You'd need to use X-ray crystallography or NMR to get that type of resolution, both of which are still out of reach for the DIY biologist. However, if the structure of your protein of interest has already been found (search pdb.org for your protein), then you are in business. Alternatively, if your protein of interest has enough sequence similarity to proteins with known structures, you can build a homology model (e.g. http://swissmodel.expasy.org/).
Once you have a structure model, you can start o try to dock various compounds computationally to try to find a hit. A lot of the software to do this type of modeling is ridiculously expensive. Thankfully, there are some free/open-source options available. Check out http://autodock.scripps.edu/ for one option.
This is one of the basic workflows that large pharmaceutical companies use to find new drug candidates. It works, but they end up investing millions of dollars to make it work. It's important to understand that computational modeling of macromolecules like protein is still very crude, and there is no guarantee that the results are accurate. You might go through a million compounds in the computer to find 100 compounds that look good in the models to find one that performs well in live cells.
On Thu, Dec 10, 2015 at 3:05 AM Brian Degger <brian.degger@gmail.com> wrote:
I reccomend going to your local biohackers space (like genspace nyc) growing your first colorful bacteria and talk about your ideas.
On 10 Dec 2015 08:31, "Nathan McCorkle" <nmz787@gmail.com> wrote:--To see molecules sounds a lot like wanting to see atoms. Currently the people are doing things with scanning electron microscopes (and also scanning transmission electron microscopes) where you scan a surface and analyse the xrays that are emitted as a result of the electron beam impact. There are also people that look at the energy loss of electrons that bounced off (EELS).
Then there are environmental SEMs that can operate at high enough vacuum that cells can survive (so imaging can take place, then the cells returned to their normal growth chamber).
Then there is combination FIB +SEM serial block face sectioning... You end up with a 3D image dataset. In this technique an image is acquired, then the FIB is used like a machine-shop belt-sander to grind off (ablate) a layer, then another image is acquired, and the process repeats until the sample is gone through. This has to happen at cryo freezing temperatures, otherwise the molecules will move and the images will be blurred, not to mention the sequence of images in the serial block face operation.
And there's also cryo TEM tomography, where a cell or section/slice of a cell is in a frozen state and put into the TEM and an image is acquired. If the slice is too thick (which is the use-case for this technique) it will be blurry, but with math this can be unblurred into a 3D volume dataset. This is kind of like diffraction crystallography.
On Dec 9, 2015 8:59 PM, "coolcash2004" <davidconwayj@gmail.com> wrote:----Hi - I am new to biotech (though not to entrepreneurship in general). I have a whole bunch of DIY questions that I am saving for later - for now I've just been doing a lot of research on my own trying to determine how I want to start and planning everything out. Any help with the questions below would be greatly appreciated.1 - For a DIY lab, is it possible to view bacteria on the molecular level? Separately, is it possible to view them while changing (pre treatment, during, and post) on a molecular level? Is the equipment needed for this reasonably priced? Is it ever possible to rent or borrow equipment? (The microscopes I saw online seemed to cost $25,000+ but I can't imagine thats the only way - or I'm looking at the wrong machines).2 - If I were to take the findings from part 1 (and have a detailed view of the bacteria in various states) is it possible to then design a new compound that will accomplish something specific with the bacteria WITHOUT taking existing compounds and without actually doing the lab testing for now? And what would be the best way to approach this? Is molecular modeling the best way to go? Is it reasonable to learn as much as I can about various compounds, etc and then model a new compound from a problem solving approach rather than looking at existing compounds? (Assume to date all existing compounds tested have failed). Where should I look to begin learning the basics of how to engineer compounds? Any links are appreciated. School is not an option at this point. I understand the process in general of looking at bacteria, finding targets, then design compound that will achieve goals within parameters - but I'm struggling to find info on how you actually design a compound (without just testing existing compounds for potential matches).3 - Is the NYC group I saw here still active? It would be great to meet with other people from NYC at some point later on.Thank you so much. Any other feedback / resources are appreciated as well.
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