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Table 2 Configurable parameters for each algorithm and their optimal values

From: Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

Algorithm Parameter Optimal Value*
MCL Inflation 3.6
MCODE Include Loops FALSE
  Degree Cut-off 2
  Haircut TRUE
  Fluff FALSE
  Node Score Cut-off 0
  K-Core 2
  Max. Depth 100
Clustering Coefficient - 0.4
  1. * For MCODE and clustering coefficient, the values are optimized for precision. For MCL, the inflation parameter is optimized for recall, because it showed the same degree of precision at all inflation values.