Hi Everyone, in this demo I'll introduce ChemoGraph -
A novel visual analytics technique to interactively explore the chemical space.
Here is the visual interface of the ChemoGraph. Users start their exploration of the chemical
space from the top control panel. There are two different ways to give inputs to the tool.
First one is by importing files. ChemoGraph currently supports Json and SMI file formats.
Importing them will set up the initial view.
Another way is to start by using command strings. We can either give an entire
command or simply a compound and hit submit, to see its scaffold class.
Here, I started with a lead compound identified from one of the high throughput
virtual screening studies. This string representation is called a SMILE string,
one of the common ways to represent chemical compounds. To get an idea of some sample compounds
in this scaffold class we can run an "expand" operation. Give a sample size and run "expand".
Users can decompose a scaffold into sub scaffolds by performing an operation called "lower". Select
the scaffold and then the operation. Similarly, users can create super scaffolds by using an
operation called "upper". Users can perform these operations iteratively and can export the
resulting networks. This helps the users to resume their exploration by loading a specific state.
Now, I am loading a previously saved state that I'll be using for the reminder of this demo.
This process of starting from A lead compound and elaborating it into a series of local
chemistries is useful in the generation of a Structure Activity Relationship (SAR) series,
where current practices involve by-hand enumeration, which is time consuming.
With this visual interface users can do it easily while controlling the
series generation depending on various attributes.
Here, we can see each scaffold is associated with two properties - the first one is log P value
and the second one is SA score. These levels here represent the complexity of scaffolds.
Lower the number of rings, simpler the scaffolds. As
the level increases number of rings in corresponding scaffolds also increase.
This organization helps us in giving a spatial structure to the scaffolds in the chemical space.
Each level in ChemoGraph can be independently sorted by a numerical attribute that is selected
from the Legend. Here, log P value is selected. Hence, clicking on the level
label toggles between different ways of reordering, based on the log P value.
Also, changing to SA score updates all the levels correspondingly.
Users can hover on a scaffold to see the directly related scaffolds.
Selecting a scaffold highlights all the related scaffolds across all the levels.
Changes in the states, either for nodes or edges,
can be clearly identified from the color highlights.
This helps users to quickly identify both complex and simple scaffolds related to the selected one.
Zoom interaction is used to identify selected scaffold as a substructure in the higher levels.
In all the upper levels of selected scaffold, if the selected scaffold is present,
zoom operation highlights the structure of the selected scaffold using a red color stroke.
One of the important aspects of ChemoGraph is to provide
the ability to take custom user trained biophysical property models as input,
and encode them on the scaffolds. By default, we have two common properties for each node here.
But users can easily add their own models through the API and the interface shows them here.
So a user can select the model, and it can be encoded on the nodes in the network.
Once a custom model is added onto all the nodes in the network, it can also be used
as any of the existing properties like log P or SA score. For example, here selecting "model 1"
updates all the levels and the reordering stages based on the selected model. Finally, once the
exploration is completed, users can export either the smile strings along with encoded properties
into an SMI file or export the entire view as the checkpoint and resume their exploration in future.
Thank you for watching the demo of our tool ChemoGraph. If you want to try ChemoGraph,
you can access the tool at this URL.