molclaw-linker-sampling

To generate linker molecules for PROTAC design, provide two warhead fragments with exactly one attachment point each and specify the number of candidates to sample. The tool outputs SMILES strings for the resulting bivalent ligand structures.

Designing linkers for fragment merging requires specifying warhead fragments with single attachment points and desired sample size. You can enforce linker-length constraints and apply Lipinski-like filters to ensure generated candidates meet drug-like quality standards.

Yes, you can use predefined warhead pairs for bivalent ligand sampling by selecting a predefined pair name and specifying the sample size. This enables rapid linker exploration and benchmarking without manually defining custom warhead fragments.

When sampling linker candidates between warheads, you can apply minimum and maximum linker atom constraints alongside Lipinski-like molecular filters. These quality controls ensure generated linker scaffolds adhere to early-stage drug discovery parameters.

Yes, warhead fragments require exactly one attachment point for linker generation. The tool uses this single connection site to properly join the two warhead fragments with the sampled linker molecule.

You should sample an integer number of linker candidates based on your exploration needs, such as 50 candidates to connect a benzene warhead to a piperazine warhead. Specify this integer to control the volume of generated SMILES structures.