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Table 1 Active and passive AIRs chosen for the docking experiments

From: MTMDAT-HADDOCK: High-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry

Active and passive AIRs
Docking Run active AIRs passive AIRs
Baseline (BL)   
Rpn13 S55, L56, L73, I74, auto
  F76, P77, D78, D79,  
  K99, A100, G101  
ubiquitin K6, L8, I44, F45, auto
  A46, G47, K48, Q49,  
  H68, V70, R72  
LP/MS filter (Ubiquitin CPORT)   
Rpn13 D41, K42, D53, D54, auto
  E70, D79, E81, K99  
ubiquitin - F4, K6-K11, P19, Q31,
   E34-Q40, R42, I44-Q49, R54,
   T55, S57-N60, Q62-T66, H68,
   V70, L71-G76
LP/MS (Ubiquitin CPORT)   
Rpn13 D53, D54, S55, D78, auto
  D79, F98, K99  
ubiquitin - F4, K6-K11, P19, Q31,
   E34-Q40, R42, I44-Q49, R54,
   T55, S57-N60, Q62-T66, H68,
   V70, L71-G76
chemical shift perturbations   
Rpn13 S55, F76, D78, K99, auto
  G101, R104  
ubiquitin L8, F45, A46, G47, auto
  K48, Q49, H68, V70  
CPORT   
Rpn13 Y22-E25, R27, M31, auto
  T36-P40, Q50-L56, H58,  
  V69, D71-I74,  
  F76, P77, D79, V85, C88-S90,  
  V93, V95, K103, L105, F106,  
  W108, E126, C127, N129, N130  
ubiquitin F4, K6-K11, P19, Q31, auto
  E34-Q40, R42, I44-Q49, R54,  
  T55, S57-N60, Q62-T66, H68,  
  V70, L71-G76