Enumerate the protonation states of each small molecule that are plausible at a target pH with Dimorphite-DL, optionally with RDKit tautomers, and estimate each state's relative population from Henderson–Hasselbalch fractions at its sites. Every state keeps its parent's InChIKey, net charge, and population, so docking, MM-GBSA, and force-field steps can run per state and still compare results by parent. Site pKa values are typical values for each functional-group type, not measured or predicted for your molecule, so treat populations as estimates.
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Estimated minimum cost: $—
Examples
Molecules
Paste SMILES or InChI one per line, or mol blocks / SDF records. At most 10,000 molecules. Each entry must be a single parent: salts and mixtures are rejected, so run the Molecule Standardizer first to strip counter-ions.
or drop a file here
State options
Molecules × max states per molecule must not exceed 200,000.