Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

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…

DCA
Algorithm

DCA Dynamic Core-Attachment

Identifies protein complexes by integrating their inherent organizations into…

Identifies protein complexes by integrating their inherent organizations into dynamic protein-protein interaction (PPI) network. DCA generates protein complexes by appending attachments into the…

HernandezEtAl20…
Desktop

HernandezEtAl2017

Predicts protein complexes by using dense subgraphs built from complete…

Predicts protein complexes by using dense subgraphs built from complete bipartite graph patterns. The software creates protein-protein interaction (PPI) networks as directed acyclic graphs, which…

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…

BFO-FMD
Algorithm

BFO-FMD Bacterial Foraging Optimization for Functional Module Detection

Serves functional module detection in PPI networks. BFO-FMD works in three…

Serves functional module detection in PPI networks. BFO-FMD works in three stages: solution initialization, solution optimization, and post-processing. First, it constructs each bacterial individual…

CommWalker
Desktop

CommWalker

Allows users to study poorly-studied network regions, without sacrificing its…

Allows users to study poorly-studied network regions, without sacrificing its ability to faithfully evaluate well-studied communities. CommWalker is a module evaluation framework that takes this…

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…

PCD-GED
Algorithm

PCD-GED

Calculates a simple active threshold for each gene, based on its mean of…

Calculates a simple active threshold for each gene, based on its mean of expression profile. PCD-GED continues with generating a series of subnetworks of active proteins according to each column of…

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…

HOPACH
Desktop

HOPACH Hierarchical Ordered Partitioning And Collapsing Hybrid

Addresses some of the short comings of currently available methods for…

Addresses some of the short comings of currently available methods for clustering gene expression data. HOPACH constructs a hierarchical tree whose final level is an ordered list of elements. It…

Dynamic Tree…
Desktop

Dynamic Tree Cut

Recognizes branches that could not have been identified using the static cut…

Recognizes branches that could not have been identified using the static cut method. Dynamic Tree Cut is based on analyzing the shape of the branches of a dendrogram. It relies solely on the…

ACC-FMD
Algorithm

ACC-FMD Ant Colony Clustering for Functional Module Detection

Allows detection of functional modules. ACC-FMD is an algorithm adopting an ant…

Allows detection of functional modules. ACC-FMD is an algorithm adopting an ant colony clustering model to mine functional modules in protein-protein interaction (PPI) networks. First, it calculates…

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…

SurpriseMe
Desktop

SurpriseMe

Accelerates the research process. SurpriseMe is composed of several algorithms…

Accelerates the research process. SurpriseMe is composed of several algorithms and calculates distances among the solutions provided by the algorithms. It supplies users distance matrices (with…

MAE-FMD
Desktop

MAE-FMD Multi-Agent Evolutionary method for Functional Module Detection

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

Detects functional modules in protein-protein interaction (PPI) networks. MAE-FMD employs a group of agents as a population to carry out random walks from a start protein to other proteins in a PPI…

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…

RNSC
Algorithm

RNSC Restricted Neighborhood Search Clustering Algorithm

Identifies and predicts protein complexes. RNSC relies on modeling the…

Identifies and predicts protein complexes. RNSC relies on modeling the protein-protein interaction (PPI) network with a graph where nodes represent proteins and edges correspond to interactions. It…

ABC algorithm
Desktop

ABC algorithm Artificial Bee Colony algorithm

Determines cluster number and eliminates the noise spots. ABC algorithm is a…

Determines cluster number and eliminates the noise spots. ABC algorithm is a flow clustering method that can select cluster centers. It operates according to a well-defined process: first, it…

Jerarca
Desktop

Jerarca

Contains algorithms to perform iterative hierarchical cluster analyses:…

Contains algorithms to perform iterative hierarchical cluster analyses: UVCluster, RCluster and SCluster. Jerarca provides alternative ways to obtain the matrices of secondary distances from a graph.…

SR-MCL
Algorithm

SR-MCL Soft Regularized-Markov CLustering

Allows detections both the parent module as well as the child module in the…

Allows detections both the parent module as well as the child module in the gene ontology (GO) hierarchy. SR-MCL is an algorithm assisting users to find functional modules or protein complexes to…

HAM-FMD
Algorithm

HAM-FMD

Allows identification of functional modules in protein-protein interaction…

Allows identification of functional modules in protein-protein interaction (PPI) networks. HAM-FMD is based on ant colony optimization and multi-agent evolution (ACO-MAE). This tool focuses on the…

ACO-MAE
Algorithm

ACO-MAE Ant Colony Optimization with Multi-Agent Evolution

Assists in identification of functional module. ACO-MAE is an algorithm…

Assists in identification of functional module. ACO-MAE is an algorithm improving performance of ant colony optimization (ACO) by integrating multi agent evolution (MAE). This tool works according to…

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…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.