Entity Relation Map

Entity notes define what object a model is operating on. In Molecular Modeling, the same model family can mean different things depending on whether the unit is a molecule, protein, pocket, complex, assay row, or dataset.

The central relation for structure-based modeling is:

$$\text{protein}+\text{pocket}+\text{ligand}\to \text{protein-ligand complex}$$

The central relation for supervised chem-bio ML is:

$$(\text{molecule},\text{target},\text{assay})\to \text{bioactivity label}$$

This is the Target-assay-label contract.

Object Hierarchy

• Molecule is the general chemical object.
• Ligand is a molecule considered as a binding partner.
• Target is the biological object a task is centered on.
• Protein is the biological target or modeled macromolecule.
• Pocket is a local region of a protein.
• Protein-ligand complex combines ligand pose and protein context.
• Assay defines how a label was measured.
• Bioactivity label records the measured or curated response.
• Dataset collects examples, labels, metadata, and splits.
• Target-assay-label contract connects the measured object, measurement protocol, label semantics, and split rule.

Representation Choices

• Sequence: residues, nucleotides, SMILES tokens, or k-mers.
• Graph: atoms, residues, bonds, contacts, or interaction edges.
• Structure: 3D coordinates, distances, local frames, surfaces, or voxels.
• Metadata: assay protocol, source, target, assembly, or split group.

Split Units

The split unit should match the generalization claim:

• Molecule-side generalization: scaffold or molecular cluster.
• Protein-side generalization: sequence or structure family.
• Complex-side generalization: both ligand scaffold and protein family.
• Assay-side generalization: assay, campaign, target, or source group.
• Genome-side generalization: region, chromosome, species, or source group.

Checks

• What is one example?
• What is the target label?
• What target, assay, and context produced the label?
• Is the label assay-conditioned, target-conditioned, censored, transformed, or thresholded?
• Which entities are inputs and which are metadata?
• Which entity defines the split group?
• Could the same molecule, homologous protein, related complex, or shared assay leak across splits?
• Does the representation preserve the chemistry or geometry needed for the task?

Related

• Computational Biology
• Target
• Target-assay-label contract
• Bioactivity label
• Data
• Leakage
• Scaffold split
• Protein family split
• Structure-based drug discovery