CAMWI: Detecting protein complexes using weighted clustering coefficient and weighted density

BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes

“…Then, we compared dynamic extension of several protein complex detection methods using the genetic-based biclustering algorithm. The results of this comparison encourage us to suggest BiCAMWI, the dynamic variant of previous proposed method CAMWI[ 56 ] as more reliable method for protein complex detection. Finally, we compared BiCAMWI with other detection methods, both static and dynamic methods.…”

“…To have a better view of the proposed genetic-based algorithm advantages, in this subsection, we compare our proposed biclustering method, GA-DCT, with some popular biclustering algorithms CC[ 39 ], BiMax[ 44 ], xMOTISs[ 46 ], OPSM[ 47 ],ISA[ 48 ] and UniBic[ 65 ]. in all methods, after producing biclusters and extracting dynamic subnetworks, CAMWI method[ 56 ] is used to detect protein complexes from every dynamic PPI subnetwork. Aggregating the results after removing duplicate complexes produces the final set of detected protein complexes.…”

“…To show how effectively the proposed method improves the accuracy of protein complex detection methods, we compare the results obtained from running several recent methods, CAMWI[ 56 ], COACH [ 66 ], ClusterONE [ 14 ], SPICi [ 67 ] and MCL [ 68 ] on three modes: 1) using static variation of methods (with fine-tuning of their parameters), 2) using dynamic variation of methods according to recent dynamic approach presented in TS-OCD, 3) using dynamic variation of methods according to the proposed approach in this paper.…”

“…Experimental results show that the proposed dynamicity based on novel biclustering algorithm, can retrieve more significant dynamic subnetworks (means subnetworks that are involved by more protein complexes) from static PPI networks and improves the accuracy of protein complex detection methods. Specially, BiCAMWI, that is a dynamic version of previously presented method, CAMWI[ 56 ], achieves significantly better results than TS-OCD and the other state-of-the-art methods. So, we suggest BiCAMWI as a more reliable method for protein complex detection.…”

DPCT: A Dynamic Method for Detecting Protein Complexes From TAP-Aware Weighted PPI Network

“…A protein is considered an attachment to a core if adding it to the core increases the weight of the total complex. CAMWI (Lakizadeh et al, 2015a ), a core-attachment based algorithm, detects protein complexes in four steps. First, it chooses seeds to find cores based on a threshold; then, seeds are grown up to make cores and in the third step it adds attachment proteins to each core.…”