Small Molecule Design Tool

The highly anticipated updates to the Small Molecule Design Tool are here, and we have a series of puzzles on the way! Your continued efforts in protein design have been nothing short of remarkable, and we are excited to be able to further help this amazing community contribute to small molecule design. While protein based drugs are an increasingly important category of therapeutics, the majority of drugs continue to be small-molecule based. With the Small Molecule Design tool you will be able to create, edit, and enhance small molecules.

Let's dive in and see how the Small Molecule Design Tool works. The tool will come up as an option in the Selection Mode action bar when you select a designable small molecule on a puzzle which supports it. With the Small Molecule Design Tool open, you can select particular atoms in the designable ligand to act on. The tool has two distinct panels: Atom Selection and Fragment Selection. You can toggle between them with the central Panel Selection Button.

The Atom Selection Panel has two unique areas: The Atom Selection area at the top and the Bond Selection area in the middle. With Atom Selection, selected atoms can be replaced with an atom of your choosing, assuming the placement is allowed. With Bond Selection, you will be able to select two atoms, and change the bond type between them.

The Fragment Selection Panel works with groups of atoms. The category buttons in the middle organize the fragments into four separate groups: Functional Groups, Unsaturated Cyclic, Saturated Cyclic, and Polycyclic. Each choice will change the contents of the Fragment Selection area above. Once you’ve selected the type of fragment, you can select the location (the atoms) on the small molecule where you want it to go, and then select which fragment you want from the Fragment Selection area. This will pop up a sub-panel which allows you to select where on the fragment you want to place the attachment. Using the `A`, `S` and `TAB` keys while hovering over the selection in the subpanel will allow you to further customize how the fragment is placed.

You may have noticed that both panels share a couple of elements. These are the Panel Selection Button, which allows you to switch between the Atom Selection Panel and the Fragment Selection Panel, and the Cleanup Structure area, with which you can delete atoms, delete bonds, and deselect highlighted atoms.

Be sure to check out the new tutorials to help get you started! We can't wait to see what all you come up with. Happy building!

( Posted by  Sciren 70 96  |  Tue, 10/12/2021 - 21:45  |  2 comments )
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cas0362's picture
User offline. Last seen 10 hours 13 min ago. Offline
Joined: 08/15/2017
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Fun with fragments not working ?

The fun with fragments tutorial does not appear to be working at the moment. It has a red outline.

Sciren's picture
User offline. Last seen 7 hours 50 min ago. Offline
Joined: 06/29/2019
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Fun with Fragments tutorial

Hi cas0362! I'm sorry you are experiencing an issue with the Fun with Fragments tutorial. If I could, I would like to get some more information on what you are seeing. Have you completed the Inside the Pocket tutorial? Fun with Fragments is only accessible once you have completed the previous tutorial. If you haven't, it is by design that you would see a red outline with an inactive/darker image, and be unable to play the tutorial.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons