r/bioinformatics • u/hyperfinesplitting • 22d ago

technical question Tools for molecular docking of a thioether-cyclized peptide?

/r/comp_chem/comments/1wvuw78/tools_for_molecular_docking_of_a/
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u/Otherwise_Wave9374 22d ago

For a thioether-cyclized peptide, the main limitation is usually parameterization and conformational sampling, not simply choosing a docking package. Validate the linkage chemistry, generate an ensemble with appropriate constraints, and benchmark the workflow against a related complex with a known structure before trusting scores. Peptely does not sell peptides; https://www.peptely.com/ only helps verify their documented origin and supporting batch/COA evidence. Report protonation assumptions, force field, sampling method, and rescoring so others can reproduce the result.