| id,protein_context,alphafold_signals,proposed_inference,gold_misinterpretation,gold_error_type,gold_correction | |
| 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" | |