data/test.csv

id,protein_context,alphafold_signals,proposed_inference,gold_misinterpretation,gold_error_type,gold_correction
AFMC-T01,"signaling protein tail","pLDDT:tail=30 core=90; disorder:high","Tail adopts a stable fold suitable for docking","yes","low_confidence_region_overtrust","Do not dock to low pLDDT disordered tail. Use sequence motifs and experiments"
AFMC-T02,"two-domain regulator","pLDDT:domains=86; PAE:interdomain-high","Domain orientation is fixed and defines function","yes","interdomain_orientation_overclaim","High interdomain PAE suggests flexible orientation. Validate with SAXS or other methods"
AFMC-T03,"enzyme with known ligand","pLDDT:90; ligands:none; experimental:binding_known","Model proves ligand does not bind because no ligand shown","yes","cofactor_absence_misread","AlphaFold does not include ligands by default. Use experimental binding data and docking cautiously"
AFMC-T04,"possible homodimer","pLDDT:monomer=88; oligomer_context:unknown","Monomer prediction rules out dimerization","yes","complex_negation_from_monomer","Monomer model cannot rule out dimers. Use multimer prediction or experiments"
AFMC-T05,"globular enzyme","pLDDT:overall=92; PAE:low","Fold appears reliable for residue mapping and hypothesis generation","no","no_error","Proceed for mapping and hypotheses. Confirm critical claims with experiments"
AFMC-T06,"membrane receptor extracellular loop","pLDDT:loop=38 TM=85; PAE:loop-high","Loop epitope is precise for antibody design","yes","loop_position_overtrust","Avoid precise loop claims. Validate loop conformation experimentally"
AFMC-T07,"predicted interface","pLDDT:interface=62; PAE:interface-high","Interface geometry is stable and defines binding pocket","yes","interface_overconfidence","Treat interface as uncertain. Use co-folding and validation"
AFMC-T08,"IDR with short helix","pLDDT:IDR=22; disorder:high","Short helix means stable structured domain","yes","disorder_as_structure","Low pLDDT with high disorder supports IDR. Avoid stable-domain claims"
AFMC-T09,"enzyme active site loop","pLDDT:loop=45 core=93; PAE:loop-high","Loop positions are accurate enough for precise docking constraints","yes","low_confidence_region_overtrust","Do not constrain docking on uncertain loop. Focus on core or validate loop"
AFMC-T10,"protein with strong experimental agreement","pLDDT:89; PAE:low; experimental:xray_agrees","Model can be used as supportive structural reference","no","no_error","Use as supportive reference with citation of experimental agreement"