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The Small Molecule Design category covers the tools and concepts used in Foldit small molecule design puzzles.

The terms "small molecule design" and "ligand design" are used interchangeably and inconsistently in Foldit. In small molecule design puzzles, the ligand is the non-protein part that's being designed. The ligand needs to bind to a protein in these puzzles, but the protein is likely to be completely locked. (In some cases, a few protein sidechains may be unlocked and able to move.)

The term drug design was also previously used for this type of puzzle. The meaning is the same.

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