Drug Design Update: Tool Talk
We are now ready to deploy a series of tools for small molecule drug discovery! Our goal is to release new tools on a rolling basis for the next couple of weeks. Because the tools are still being tested and not guaranteed to be bug free, we have created an “experimental” user group. This user group is open to everyone who wants to test the drug discovery tools; however, we do ask, that you report any bugs that you find or any suggestions that you have for the interface. After all the tools have been tested, we will release the drug discovery tools to Foldit’s main client.
You should expect this build to be experimental. This means that you have a chance of losing your designs. Because of this, it is highly recommend that you keep a separate install outside of your main client. This will ensure that you do not lose your main game puzzle progress.
In order to get access for the experimental group, follow the steps for access to the devprev build. Instead of replacing “main” with “devprev” in the options.txt file, type “experimental”.
"update_group" : "experimental"
The first tool is a very simple tool and is an expansion of the very first puzzle’s tool released for small molecule drug discovery. It is simply named, “Ligand Design Tool”. This tool provides the ability to change the identity of elements, create bonds between atoms, add a predefined set of fragments, delete atoms, and delete bonds. The Ligand Design Tool is available in both the Selection Interface and in the original Foldit interface.
You may want to change your view to the ligand design view. This will let you see the hydrogens on the small molecule, which can be used to extend the ligand by a single atom. You can access this by changing the view options in the advanced options menu.
In addition to releasing the first tool, we have three new tutorials. The tutorials are a work in progress and will be updated when we have some down time. The tutorials are particularly exciting as they follow the progression of a scientific team as they design an inhibitor for the FKB binding protein.
The puzzle that we are using for testing is Dihydrofulate Reductase (DHFR). Read on to get some more information on DHFR!
Finally, here is what to expect in the upcoming weeks. We will have a new blog post for each topic explaining in detail the science behind each tool and the tool's purpose:
Ligand minimization with a new force field, MMFF, and a set of new filters to guide you in designing small molecules, the rule of five filter and a similarity filter. We will have an explanation of all these features later on, but here is a video of the MMFF minimization.
There is also the ligand queueing interface. This tool allows us to give you small molecules that have been pre-identified (through experiments or virtual high throughput screening) that might bind in the target protein. This tool will also allow you to share your small molecule designs between your teams.
Finally, we are also creating a tool that lets you design small molecules like medicinal chemists. This is called reaction based drug design and provides a synthetic pathway for organic chemists to design the small molecule you create.
Additionally, I should be around in chat on Friday (April 29, 2016) around 2PM Eastern to help answer questions! Think of it like an "office hour", where you can drop in and get things answered versus an actual scientist chat.