Deterministic in-silico physicochemical descriptors, calculated from each peptide's sequence or chemical structure (RDKit) and validated against independent reference implementations. They complement the measured ADMET endpoints; every value is shown per peptide on its detail page with a “computed” label.
atlas-seq-descriptors v1
Sum of polar (N,O) surface contributions. Strong correlate of passive permeability and oral absorption. Exact match vs CycPeptMPDB precomputed.
RDKit 2026.03.2 (Descriptors.TPSA)
Atom-contribution computed logP. COMPUTED descriptor — NOT the measured logD endpoint (ATLXE0000020). Exact match vs CycPeptMPDB precomputed.
RDKit 2026.03.2 (Crippen.MolLogP)
Count of N-H and O-H donors (Lipinski Rule-of-5 definition). For cyclic peptides, the dominant single determinant of passive membrane permeability. 100% match vs CycPeptMPDB.
RDKit 2026.03.2 (Lipinski.NumHDonors)
Count of N/O acceptors (Lipinski Rule-of-5 definition). Validated vs CycPeptMPDB (refined RDKit definition).
RDKit 2026.03.2 (Lipinski.NumHAcceptors)
Non-ring single bonds to non-terminal heavy atoms, EXCLUDING amide C–N bonds (Veber strict definition; confirmed on reference molecules). Macrocycle ring bonds excluded by definition.
RDKit 2026.03.2 (CalcNumRotatableBonds, Strict)
Count of Lipinski Ro5 violations (MW≤500, cLogP≤5, HBD≤5, HBA≤10). bRo5 oral-space classification (Doak 2014) carried in payload. Developability framing for macrocyclic peptides.
atlas-derived v1
