Linker libraries, ternary complex coordinates, DC50 predictions, Dmax scores, and hook effect assessments.

These tools return linker libraries with drug-likeness properties, ternary complex 3D coordinates, and degradation metrics like DC50, Dmax, and hook effect risk — letting you rank degrader candidates and carry the most feasible ones into ADMET, retrosynthesis, and docking validation.

Interpreting PROTAC outputs

PROTAC Linker Enumerate output

Field	Type	Description
`warhead_smiles`	string	Input warhead SMILES
`e3_ligand_smiles`	string	Input E3 ligand SMILES
`e3_system`	string	E3 ligase system used
`total_linkers`	number	Number of linkers generated
`scaffold_distribution`	object	Count of linkers per scaffold type
`linkers`	array	Individual linker results

Linker fields

Field	Type	Description
`linker_smiles`	string	SMILES of the linker fragment
`full_protac_smiles`	string	SMILES of the complete PROTAC (warhead-linker-E3 ligand)
`linker_length`	number	Atom count in shortest linker path
`rotatable_bonds`	number	Number of rotatable bonds in the linker
`scaffold_type`	string	Linker scaffold classification
`molecular_weight`	number	Total PROTAC molecular weight (Da)
`clogp`	number	Calculated partition coefficient
`tpsa`	number	Topological polar surface area (A^2)
`hbd`	number	Hydrogen bond donors
`hba`	number	Hydrogen bond acceptors
`qed`	number	Quantitative estimate of drug-likeness (0-1)
`sa_score`	number	Synthetic accessibility score (1-10, lower = easier)
`diversity_rank`	number	Rank by chemical diversity within the library

Scaffold distribution example

{
  "peg": 15,
  "alkyl": 12,
  "piperazine": 10,
  "triazole": 8,
  "hybrid": 5
}

Drug-likeness considerations for PROTACs

PROTACs violate Lipinski's Rule of Five due to their large size. Use PROTAC-specific guidelines:

Property	Traditional drug	PROTAC acceptable range
Molecular weight	< 500 Da	700-1200 Da
cLogP	< 5	< 10
HBD	< 5	< 8
HBA	< 10	< 18
TPSA	< 140 A^2	< 300 A^2
Rotatable bonds	< 10	< 20

PROTAC Ternary Model output

Field	Type	Description
`protac_smiles`	string	Input PROTAC SMILES
`poi_structure`	string	POI structure identifier
`e3_structure`	string	E3 ligase structure identifier
`e3_system`	string	E3 ligase system
`num_conformers`	number	Number of conformers sampled
`best_conformer`	object	Top-scoring ternary complex
`conformers`	array	All conformer results
`complex_pdb_url`	string	Download URL for the best complex PDB file

Conformer fields

Field	Type	Description
`conformer_id`	number	Conformer index (1-based)
`feasibility_score`	number	Overall feasibility score (0-1, higher = better)
`buried_surface_area`	number	Buried surface area at POI-E3 interface (A^2)
`shape_complementarity`	number	Shape complementarity score (0-1)
`clash_count`	number	Number of steric clashes
`interface_residues_poi`	number	POI residues at the interface
`interface_residues_e3`	number	E3 ligase residues at the interface
`linker_strain_energy`	number	Linker conformational strain (kcal/mol)
`pdb_url`	string	Download URL for this conformer's PDB file

Feasibility score interpretation

Score Range	Interpretation
0.8 - 1.0	Excellent: strong productive interface, minimal clashes
0.6 - 0.8	Good: reasonable interface, proceed to degradation scoring
0.4 - 0.6	Marginal: weak interface, consider linker modifications
< 0.4	Poor: unlikely to form productive ternary complex

Buried surface area interpretation

BSA Range (A^2)	Interpretation
> 2000	Large, stable interface
1500 - 2000	Moderate interface, typical for productive PROTACs
1000 - 1500	Small interface, may require optimization
< 1000	Minimal interface, likely non-productive

PROTAC Degradation Score output

Field	Type	Description
`protac_smiles`	string	Input PROTAC SMILES
`e3_system`	string	E3 ligase system
`dc50_nm`	number	Predicted DC50 in nanomolar
`dmax_pct`	number	Predicted maximum degradation percentage
`hook_effect_risk`	string	Hook effect risk assessment
`cooperativity_alpha`	number	Ternary complex cooperativity factor
`overall_grade`	string	Summary grade (A-F)
`component_scores`	object	Breakdown of scoring components

Component scores

Field	Type	Description
`linker_score`	number	Linker property contribution (0-1)
`ternary_score`	number	Ternary complex geometry contribution (0-1, requires ternary_job_id)
`physicochemical_score`	number	Drug-likeness contribution (0-1)
`permeability_score`	number	Predicted cell permeability (0-1)

DC50 interpretation

DC50 Range	Grade	Interpretation
< 10 nM	A	Highly potent degrader
10 - 100 nM	B	Potent degrader
100 nM - 1 uM	C	Moderate degrader
1 - 10 uM	D	Weak degrader
> 10 uM	F	Unlikely to achieve meaningful degradation

Dmax interpretation

Dmax Range	Grade	Interpretation
> 90%	A	Near-complete degradation
70 - 90%	B	Good degradation
50 - 70%	C	Partial degradation
30 - 50%	D	Limited degradation
< 30%	F	Insufficient degradation

Hook effect risk levels

Risk Level	Description
`"low"`	No bell-shaped dose-response expected
`"moderate"`	Some binary complex competition at high concentrations
`"high"`	Strong binary complex formation, expect reduced efficacy at > 1 uM

Cooperativity interpretation

Alpha Value	Interpretation
> 1.0	Positive cooperativity (ternary complex is stabilized)
1.0	No cooperativity (binding events are independent)
< 1.0	Negative cooperativity (ternary complex is destabilized)

Interpreting PROTAC outputs

Interpreting PROTAC outputs

PROTAC Linker Enumerate output

Linker fields

Scaffold distribution example

Drug-likeness considerations for PROTACs

PROTAC Ternary Model output

Conformer fields

Feasibility score interpretation

Buried surface area interpretation

PROTAC Degradation Score output

Component scores

DC50 interpretation

Dmax interpretation

Hook effect risk levels

Cooperativity interpretation

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PROTAC inputs and parameters

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