title: Improved method for protein complex detection using bottleneck proteins.
abstract: BACKGROUND
  Detecting protein complexes is one of essential and fundamental tasks in understanding various biological functions or processes. Therefore accurate identification of protein complexes is indispensable.
  
  
  METHODS
  For more accurate detection of protein complexes, we propose an algorithm which detects dense protein sub-networks of which proteins share closely located bottleneck proteins. The proposed algorithm is capable of finding protein complexes which allow overlapping with each other.
  
  
  RESULTS
  We applied our algorithm to several PPI (Protein-Protein Interaction) networks of Saccharomyces cerevisiae and Homo sapiens, and validated our results using public databases of protein complexes. The prediction accuracy was even more improved over our previous work which used also bottleneck information of the PPI network, but showed limitation when predicting small-sized protein complex detection.
  
  
  CONCLUSIONS
  Our algorithm resulted in overlapping protein complexes with significantly improved F1 score over existing algorithms. This result comes from high recall due to effective network search, as well as high precision due to proper use of bottleneck information during the network search.
authors.affiliation: Department of Computer Science, Yonsei University, 3rd Engineering Bldg, 533-1, Shinchon-dong, Seodaemun-gu, Seoul, Korea.
authors.forename: Jaegyoon
authors.initials: J
authors.lastname: Ahn
authors.forename: Dae Hyun
authors.initials: DH
authors.lastname: Lee
authors.forename: Youngmi
authors.initials: Y
authors.lastname: Yoon
authors.forename: Yunku
authors.initials: Y
authors.lastname: Yeu
authors.forename: Sanghyun
authors.initials: S
authors.lastname: Park
mesh_terms: D000465:Algorithms; D001686:Biological Phenomena / Q000502:physiology*; D016000:Cluster Analysis; D019295:Computational Biology; D006801:Humans; D008954:Models, Biological; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000592:standards*; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology*
chemical_list: D029701:Saccharomyces cerevisiae Proteins