A small molecule is highlighted by the X-ray tunnel feature. Some of the small molecule tools are visible.
Small molecule design puzzles present a protein and a small molecule or ligand. Unlike other Foldit design puzzles, changes to the protein are limited, but a new set of tools is available for changing the small molecule.
Small molecule design was originally referred to as "drug design", since one application would be designing drugs to target proteins associated with diseases.
Small molecule design has been in development for several years in Foldit, but has been held back by technical challenges.
A new version of small molecule design released in late 2021 substantially updated the small molecule design tools. The VHL ligand design puzzles were the first to use the new interface.
Most of the small molecule design features work with the original interface, the selection interface, and the new interface.
In the original interface, there are two new mode available for small molecule design puzzles: Ligand Design and Ligand Properties. In the selection and new interfaces, the equivalent tools appear in the action bar when the small molecule is selected. Another tool, MMFF wiggle is available in the right-click pie menu in Pull Mode in the original interface, and on the action bar in the new and selection interfaces.
The use of the term "ligand" in may be subject to change. Some of the tools have "ligand" in the button which selects the tool, but then show "small molecule" in the title of the tool's dialog window.
In all interfaces, the ligand design feature depends on selecting one or more atoms of the small molecule or ligand. Although this is somewhat similar to selecting segments in the selection interface, the logic is different. Clicking on an atom in the ligand highlights the atom. Additional atoms become selected as you click on them. Control-clicking clears the selected atoms, as does the "broom" icon in the small molecule design window.
The X-ray tunnel for ligand feature may be helpful in revealing the small molecule when it's surrounded by protein.
See also[]
- Objective, for a description of SMD filters
Literature[]
- A good description of SMD puzzle tools is found in Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders.