Determining the minimum number of protein-protein interactions required to support known protein complexes

Natsu Nakajima, Morihiro Hayashida, Jesper Jansson, Osamu Maruyama, Tatsuya Akutsu

    Research output: Contribution to journalArticlepeer-review

    12 Citations (Scopus)

    Abstract

    The prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (additional) required protein-protein interactions as a graph theoretic problem under the constraint that each complex constitutes a connected component in a PPI network. For this problem, we develop two computational methods: one is based on integer linear programming (ILPMinPPI) and the other one is based on an existing greedy-type approximation algorithm (GreedyMinPPI) originally developed in the context of communication and social networks. Since the former method is only applicable to datasets of small size, we apply the latter method to a combination of the CYC2008 protein complex dataset and each of eight PPI datasets (STRING, MINT, BioGRID, IntAct, DIP, BIND, WI-PHI, iRefIndex). The results show that the minimum number of additional required PPIs ranges from 51 (STRING) to 964 (BIND), and that even the four best PPI databases, STRING (51), BioGRID (67), WI-PHI (93) and iRefIndex (85), do not include enough PPIs to form all CYC2008 protein complexes. We also demonstrate that the proposed problem framework and our solutions can enhance the prediction accuracy of existing PPI prediction methods. ILPMinPPI can be freely downloaded from http://sunflower.kuicr.kyoto-u.ac.jp/~nakajima/.

    Original languageEnglish
    Article numbere0195545
    JournalPloS one
    Volume13
    Issue number4
    DOIs
    Publication statusPublished - Apr 2018

    All Science Journal Classification (ASJC) codes

    • General

    Fingerprint

    Dive into the research topics of 'Determining the minimum number of protein-protein interactions required to support known protein complexes'. Together they form a unique fingerprint.

    Cite this