Sequence- and structure-derived physicochemical properties for each peptide identity.
In the atlas
These descriptors are calculated deterministically from sequence or chemical structure and appear on peptide records next to measured ADMET evidence. They describe physicochemical character — mass-related indices, polarity, lipophilicity, and simple oral-space rules — not experimental assay outcomes.
On each peptide page under physicochemical profile, when the identity has a usable sequence or structure.
10 definitions · 4 sequence · 6 structure
From the parent-residue sequence · 4 descriptors
Relative volume of aliphatic side chains: Ala% + 2.9·Val% + 3.9·(Ile%+Leu%). Higher values associate with thermostability. Validated vs peptides.py.
(10/L)·Σ DIWV(dipeptide). >40 suggests a sequence predicted unstable in vitro. Dipeptide weight table per Guruprasad 1990; exact match vs BioPython. Protein-derived — interpret cautiously for very short peptides.
Potential protein-interaction index: −Σ(side-chain solubility)/N. Proline contributes 0 (absent from the original table). Validated vs peptides.py.
ε280 (reduced) = 5500·nTrp + 1490·nTyr. Cystine-bonded form (+125 per disulfide) and A280(0.1%, 1 g/L) carried in payload. Exact match vs BioPython.
From chemical structure (SMILES / RDKit) · 6 descriptors
Sum of polar (N,O) surface contributions. Strong correlate of passive permeability and oral absorption. Exact match vs CycPeptMPDB precomputed.
Atom-contribution computed logP. COMPUTED descriptor — NOT the measured logD endpoint (ATLXE0000020). Exact match vs CycPeptMPDB precomputed.
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.
Count of N/O acceptors (Lipinski Rule-of-5 definition). Validated vs CycPeptMPDB (refined RDKit definition).
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.
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.
