The NDComplex software identifies complexes from a protein interaction network by considering complexes that reside in very dense regions and complexes that reside in regions with low neighborhood density separately.
The NDComplex software is available for download. The following steps will create a directory called ndcomplex. Detailed usage of NDComplex is provided in a README file.
Fan J.-H., Chen J. and Sze S.-H. (2012) Identifying complexes from protein interaction networks according to different types of neighborhood density. Journal of Computational Biology, 19, 1284-1294.