Profile catalogue
The six profiles in standard version 0. Each one is an independently versioned file. A released profile is never rewritten; a meaningful correction becomes a new version.
Each entry below gives what the profile carries, the representation a port has to declare to match it, the checker that runs against live values, and what passing the checker does not establish.
Inspect whatever your installed runtime actually ships:
biosimulant compatibility profiles
biosimulant compatibility show protein.sequence/v1protein.sequence/v1
One protein sequence represented as amino-acid residue symbols.
| Representation | scalar str, format sequence |
| Checker | protein_sequence |
| Context fields | species, identifier_namespace |
Passing does not establish that the sequence is biologically correct. Protein identity is not established unless an identifier namespace is declared. The profile does not translate nucleotide sequences.
chemical.smiles/v1
One molecule represented as a SMILES string.
| Representation | scalar str, format smiles |
| Checker | molecular_smiles |
| Context fields | identifier_namespace |
It does not establish tautomer, salt, protonation or canonicalization equivalence, and it does not establish that two valid strings identify the same molecule. It accepts one molecule and excludes reaction SMILES. A compatible string is not evidence that the intended molecule was supplied.
protein.multiple-sequence-alignment/v1
A protein multiple-sequence alignment in A3M form, supplied as a file.
| Representation | scalar str, file value, format a3m |
| Checker | a3m_file |
| Context fields | species, identifier_namespace |
Passing does not establish alignment quality or evolutionary appropriateness. Agreement between the alignment query and a separate protein input stays the model wrapper’s responsibility.
protein-ligand.complex-structure-mmcif/v1
A predicted three-dimensional protein-ligand complex as an mmCIF file.
| Representation | scalar str, file value, format mmcif |
| Checker | mmcif_file |
| Context fields | none |
Passing does not establish structural accuracy or biological relevance. Predicted and experimentally determined structures are not interchangeable under this profile.
boltz.binding-probability/v1
The Boltz affinity model’s affinity_probability_binary output: its reported probability that the specified ligand binds the specified protein target.
| Representation | scalar float32/float64, unit 1 |
| Checker | probability |
| Context fields | none |
This is a model prediction, not experimental evidence, and it must not be read as a clinical probability. Another model family must not claim this profile unless its output has the same reviewed meaning.
boltz.log10-ic50-micromolar/v1
The Boltz affinity model’s affinity_pred_value output: log10(IC50) with IC50 in micromolar. Lower values imply stronger predicted affinity.
| Representation | scalar float32/float64, unit 1 |
| Checker | finite_number |
| Context fields | none |
This value is not pIC50, and it is a prediction rather than a measured IC50. It is not compatible with another concentration basis or logarithmic convention without an explicit adapter.
Model-family profiles
Two of the six name a model family. affinity_pred_value means what Boltz’s documentation says it means, and a number from another model under another convention is a different quantity even when both are floats. Until someone reviews a cross-family meaning, naming the family is the honest option.
Next steps
- Use it in a model: map a port to a profile
- Propose a profile: when none of these fit
- Boltz example: all six in one lab