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Protein complex prediction software tools | Pathway analysis

Identification of protein complexes is crucial for understanding principles of cellular organization and functions. As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to…
NOVA
Desktop

NOVA

Permits to proceed analysis and visual inspection of complexome profiling (CP)…

Permits to proceed analysis and visual inspection of complexome profiling (CP) data. NOVA supports highly flexible and interactive inspection, exploration, and analysis of complexome data. It…

CytoCluster
Desktop

CytoCluster

Allows users to identify protein complexes or functional modules. CytoCluster…

Allows users to identify protein complexes or functional modules. CytoCluster is a plugin that integrates several clustering algorithms: (1) BinGO; (2) IPC-MCE; (3) DCU; (4) ClusterONE; (5) IPCA; (6)…

NCMine
Desktop

NCMine Near-Clique Mining

Identifies and visualizes functional modules with consideration of the…

Identifies and visualizes functional modules with consideration of the core-peripheral structure of modules. The core idea of the NCMine algorithm is (i) the extraction of complete subgraph-like…

DyCluster
Desktop

DyCluster

Detects protein complexes in dynamic protein interaction networks. DyCluster…

Detects protein complexes in dynamic protein interaction networks. DyCluster uses gene expression data to model protein-protein interaction (PPI) networks. It was tested using several biclustering…

BiCAMWI
Desktop

BiCAMWI

Permits to extract dynamic protein-protein interaction (PPI) subnetworks from…

Permits to extract dynamic protein-protein interaction (PPI) subnetworks from time series gene expression data. BiCAMWI applies a genetic-based biclustering algorithm on gene expression data, to…

NEOComplex
Desktop
TINCD
Desktop

TINCD Two-layer INtegrative Complex Detection

A two-layer integration framework to identify protein complexes. First, TINCD…

A two-layer integration framework to identify protein complexes. First, TINCD constructs consensus matrices for proteins and measures their co-complex propensity based on the complex knowledge…

MOEPGA
Desktop

MOEPGA MultiObjective Evolutionary Programming Genetic Algorithm

Identifies protein complexes by integrating single network topological…

Identifies protein complexes by integrating single network topological property. The MOEPGA algorithm roughly consists of three steps: it initiates the subgraph population and preprocesses data from…

DPClus
Desktop

DPClus

An algorithm for detection of protein complexes in large interaction networks.…

An algorithm for detection of protein complexes in large interaction networks. In a PPI network, a node represents a protein and an edge represents an interaction. The input to the algorithm is the…

WCOACH
Desktop

WCOACH

A graph clustering algorithm to detect protein complexes in weighted…

A graph clustering algorithm to detect protein complexes in weighted protein-protein interaction (PPI) networks. One of the well-known methods, COACH, has been improved to be compatible with weighted…

SPIN
Desktop

SPIN Simultaneous Protein Interaction Network

A network refinement model based on the structural interface data of protein…

A network refinement model based on the structural interface data of protein pairs for protein complex predictions. A simple PPI network, which is represented as a static entity, includes competitive…

SuperComplex
Desktop

SuperComplex

An algorithm for inferring protein complexes from weighted interaction graphs.…

An algorithm for inferring protein complexes from weighted interaction graphs. By using graph topological patterns and biological properties as features, we model each complex subgraph by a…

OCG
Desktop

OCG Overlapping Cluster Generator

A clustering method which decomposes a network into overlapping clusters and…

A clustering method which decomposes a network into overlapping clusters and which is, therefore, capable of correct assignment of multifunctional proteins. The principle of OCG is to cover the graph…

CFinder
Desktop

CFinder

A fast program locating and visualizing overlapping, densely interconnected…

A fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of…

MCODE
Desktop

MCODE Molecular Complex Detection

A graph theoretic clustering algorithm that detects densely connected regions…

A graph theoretic clustering algorithm that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes. The method is based on vertex…

IPCA
Desktop

IPCA

A clustering algorithm based on a new topological structure for identifying…

A clustering algorithm based on a new topological structure for identifying complexes in large protein interaction networks. The algorithm IPCA is applied to the protein interaction network of…

PINCoC
Desktop

PINCoC PPI network Co-Clustering

Searches for functional modules in protein-protein interaction (PPI) networks.…

Searches for functional modules in protein-protein interaction (PPI) networks. PINCoC is a software based on a co-clustering approach that has two advantages: the number of clusters is automatically…

RANCoC
Desktop

RANCoC

A coclustering-based technique able to generate both overlapping and…

A coclustering-based technique able to generate both overlapping and nonoverlapping clusters. The density of the clusters to search for can also be set by the user. We tested RANCoC on the two…

ClusterONE
Desktop

ClusterONE Clustering with Overlapping Neighborhood Expansion

A graph clustering algorithm that is able to handle weighted graphs and readily…

A graph clustering algorithm that is able to handle weighted graphs and readily generates overlapping clusters. Owing to these properties, ClusterONE is especially useful for detecting protein…

WPNCA
Desktop

WPNCA

Detects protein complexes from protein-protein interaction (PPI) networks.…

Detects protein complexes from protein-protein interaction (PPI) networks. WPNCA is a method that uses weighted PageRank-Nibble algorithm, which assigns adjacent nodes with different probability…

EnsemHC
Desktop

EnsemHC Ensemble Hierarchical Clustering

Allows to detect protein complexes. The EnsemHC method works with co-cluster…

Allows to detect protein complexes. The EnsemHC method works with co-cluster matrices which leverages the clustering results and the co-complex evidences from two different data sources. The…

PPISpan
Desktop

PPISpan

A frequent pattern identification technique for mining frequent functional…

A frequent pattern identification technique for mining frequent functional interaction patterns in PPI networks. We utilized molecular function Gene Ontology annotations to assign non-unique labels…

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