id
stringclasses 10
values | protein_context
stringclasses 10
values | alphafold_signals
stringclasses 10
values | proposed_inference
stringclasses 10
values | gold_misinterpretation
stringclasses 2
values | gold_error_type
stringclasses 9
values | gold_correction
stringclasses 10
values |
|---|---|---|---|---|---|---|
AFMC-001
|
enzyme active site loop
|
pLDDT:loop=42 core=92; PAE:loop-high; disorder:moderate
|
Loop geometry is precise so we can design a tight-binding inhibitor around it
|
yes
|
low_confidence_region_overtrust
|
Do not use low pLDDT loop geometry for docking. Focus on high-confidence core or validate loop experimentally
|
AFMC-002
|
soluble monomeric enzyme
|
pLDDT:overall=90; PAE:low; experimental:none
|
Structure is reliable for fold-level annotation
|
no
|
no_error
|
Use for fold annotation and cautious hypothesis generation
|
AFMC-003
|
multi-domain protein with hinge
|
pLDDT:domains=88 hinge=55; PAE:interdomain-high
|
Interdomain angle is fixed so domain arrangement is biologically locked
|
yes
|
interdomain_orientation_overclaim
|
Treat domain orientation as uncertain when PAE is high. Consider flexibility and validate with experiments
|
AFMC-004
|
intrinsically disordered region candidate
|
pLDDT:IDR=28 core=85; disorder:high
|
IDR forms a stable helix in vivo because AlphaFold shows a helix fragment
|
yes
|
disorder_as_structure
|
High disorder and low pLDDT suggest no stable fold. Use disorder tools and experiments
|
AFMC-005
|
membrane protein
|
pLDDT:TM=84 loops=40; context:membrane; experimental:none
|
All loop positions are accurate for antibody epitope mapping
|
yes
|
loop_position_overtrust
|
Use TM core as guide. Do not assume loop placement. Validate with epitope mapping experiments
|
AFMC-006
|
protein complex suspected
|
pLDDT:monomer=87; PAE:low; oligomer_context:unknown
|
Monomer model proves it does not dimerize
|
yes
|
complex_negation_from_monomer
|
Monomer prediction does not rule out oligomerization. Use AlphaFold-Multimer or experiments
|
AFMC-007
|
binding interface hypothesis
|
pLDDT:interface=60; PAE:interface-high
|
Interface residues define a stable binding pocket
|
yes
|
interface_overconfidence
|
High PAE and mid pLDDT make interface uncertain. Validate binding site with experiments or co-folding
|
AFMC-008
|
metal-binding enzyme
|
pLDDT:core=92; cofactors:none
|
Predicted pocket confirms metal coordination geometry
|
yes
|
cofactor_absence_misread
|
AlphaFold often omits cofactors. Do not infer coordination geometry without ligand or experimental data
|
AFMC-009
|
low complexity region
|
pLDDT:low_complex=25; disorder:high
|
Low complexity region forms a stable domain
|
yes
|
low_complexity_as_domain
|
Treat as disordered or context-dependent. Avoid rigid structural claims
|
AFMC-010
|
well-studied protein
|
pLDDT:88; PAE:low; experimental:known_xray_match
|
AlphaFold supports existing crystal structure alignment
|
no
|
no_error
|
Use as supportive evidence and note agreement with experiment
|
AlphaFold Misinterpretation Classifier
Purpose
Detect common ways people overclaim from AlphaFold outputs.
Input fields
- protein_context
- alphafold_signals
- proposed_inference
Required output
Return one JSON object
- misinterpretation
yes or no - error_type
must match allowed list - correction
one sentence
Allowed error_type values
- no_error
- low_confidence_region_overtrust
- interdomain_orientation_overclaim
- disorder_as_structure
- loop_position_overtrust
- complex_negation_from_monomer
- interface_overconfidence
- cofactor_absence_misread
- low_complexity_as_domain
Scoring
- misinterpretation_accuracy
- error_type_accuracy
- correction_similarity
- format_pass_rate
Run scoring
python scorer.py --predictions predictions.jsonl --test_csv data/test.csv
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