Algorithms and tools for protein–protein interaction networks clustering, with a special focus on population-based stochastic methods Clara Pizzuti1,† and Simona E. Rombo2,*,†

Algorithms and tools for protein–protein interaction networks clustering, with a special focus on population-based stochastic methods

Clara Pizzuti¹,^† and 

Simona E. Rombo, Bioinformatics 2014.

http://bioinformatics.oxfordjournals.org/content/30/10/1343.short


PR14 used 3 yeast PPI data to compare MCL with others. The MCL parameter was taken from Boheree2006. PR14 used protein complex as 'golden standard'. When overlapping score > 20%, MCL is the best algorithm. Bader's MCODE is also a good method for certain parameter settings.