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Protein-protein interaction prediction software tools | Pathway analysis

STRING
Web

STRING

Aims to provide a critical assessment and integration of protein-protein…

Aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. STRING covers more than 2000…

mentha
Web

mentha

An interactome browser that offers protein-protein physical/enzymatic…

An interactome browser that offers protein-protein physical/enzymatic interaction information integrated from various sources. Its data comes from manually curated protein-protein interaction…

GPS-Prot
Web

GPS-Prot

A software tool that allows users to easily create an integrated human protein…

A software tool that allows users to easily create an integrated human protein network, or HIV-host networks. A major advantage of this platform compared to other visualization tools is its web-based…

compPASS
Desktop

compPASS comparative proteomic analysis software suite

Allows to analyze proteomic data. The compPASS method gives confidence…

Allows to analyze proteomic data. The compPASS method gives confidence measurements to interactions from parallel non-reciprocal proteomic datasets in using unbiased metrics. This tool is applicable…

Perseus
Desktop

Perseus

Aims to proteomics data analyses. Perseus extracts biologically meaningful…

Aims to proteomics data analyses. Perseus extracts biologically meaningful information from processed raw files. It uses bioinformatic analyses from MaxQuant output and completes the proteomics…

PSICQUIC
Web

PSICQUIC Proteomics Standard Initiative Common QUery InterfaCe

It was created by the Human Proteome Organization Proteomics Standards…

It was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service…

Struct2Net
Web

Struct2Net

Makes structure-based computational predictions of protein-protein interactions…

Makes structure-based computational predictions of protein-protein interactions (PPIs). The predictions are made by a structure-based threading approach. Given two protein sequences (or one sequence…

HIPPIE
Web

HIPPIE Human Integrated Protein-Protein Interaction rEference

A human PPI dataset with a normalized scoring scheme that integrates multiple…

A human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets. HIPPIE's scoring scheme has been optimized by human experts and a computer algorithm to…

FpClass
Desktop
Web

FpClass

Predicts high-confidence protein-protein interactions (PPIs) proteome-wide,…

Predicts high-confidence protein-protein interactions (PPIs) proteome-wide, including proteins with few or no known partners. FpClass is an in-silico method to identify sets of protein features that…

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Babelomics
Desktop
Web

Babelomics

Serves for the functional analysis of gene expression and genomic data.…

Serves for the functional analysis of gene expression and genomic data. Babelomics offers the possibility to explore the effects of alteration in gene expression levels or changes in genes sequences…

APID
Web

APID Agile Protein Interaction DataAnalyzer

An interactive bioinformatic web-tool that has been developed to allow…

An interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a…

IBIS
Web

IBIS Inferred Biomolecular Interactions Server

For a given protein sequence or structure query, it reports protein-protein,…

For a given protein sequence or structure query, it reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined…

Interactome3D
Web

Interactome3D

A web application for the structural annotation of protein-protein interaction…

A web application for the structural annotation of protein-protein interaction networks. Submit your interactions and the server will find all the available structural data for both the single…

IraPPA
Web

IraPPA Integrative Ranking of Protein Protein Assemblies

Enhances the identification of near-native structures when applied to four…

Enhances the identification of near-native structures when applied to four docking methods. IraPPA is based on methods developed for Internet search ranking and electoral voting to solve the problem…

Pathway Studio
Web

Pathway Studio

An analytical solution for biological researchers and incorporates an expansive…

An analytical solution for biological researchers and incorporates an expansive knowledge base of molecular facts that enable researchers to connect independent research findings to gain new…

RedNemo
Desktop

RedNemo REpeated Diffusion with NEighborhood MOdifications

An algorithm for the topology-based reconstruction of protein-protein…

An algorithm for the topology-based reconstruction of protein-protein interaction (PPI) networks. RedNemo provides accurate networks as far as biological qualities measured in terms of most metrics…

TRI_tool
Web

TRI_tool Transcriptional Regulation Interactions

A sequence-based web tool for prediction of protein interactions in the human…

A sequence-based web tool for prediction of protein interactions in the human transcriptional regulation. TRI_tool has an improved predictive performance due to the training on updated, human…

PATH2PPI
Desktop

PATH2PPI

An R package to identify protein-protein interaction (PPI) networks for fully…

An R package to identify protein-protein interaction (PPI) networks for fully sequenced organisms for which nearly none PPI are known. PATH2PPI predicts PPI networks based on sets of proteins from…

E-coli PPI
Web

E-coli PPI

Integrates different protein-protein interaction (PPI) datasets into a reliable…

Integrates different protein-protein interaction (PPI) datasets into a reliable weighted PPI network. E.coli PPI calculates the weight of each protein pair through the highly used naïve Bayesian…

ISIPS
Desktop

ISIPS In Silico Identification of Protein Subcomplexes

Identifies the subcomplexes of a multiprotein complex. ISIPS is an in silico…

Identifies the subcomplexes of a multiprotein complex. ISIPS is an in silico approach that consists in two steps: (i) identification of proteins interacting with the subunits of the complex and (ii)…

LR_PPI
Web

LR_PPI Latent dirichlet allocation-Random forest Protein-Protein Interaction

Predicts protein-protein interactions (PPIs). LR_PPI is based on the latent…

Predicts protein-protein interactions (PPIs). LR_PPI is based on the latent topic features from amino acid sequence. It uses the generative latent dirichlet allocation (LDA) method combined with the…

atBioNet
Desktop

atBioNet

Performs network analysis followed by biological interpretation for a list of…

Performs network analysis followed by biological interpretation for a list of seed proteins/genes. atBioNet is a free web-based tool for genomic and proteomic data that has the following advantage:…

InterPreTS
Desktop
Web

InterPreTS Interaction Prediction through Tertiary Structure

A web-based tool for predicting protein-protein interactions. Given a set of…

A web-based tool for predicting protein-protein interactions. Given a set of protein sequences (in fasta format), this tool will use BLAST to find homologues of known structure for all pairs (i.e.…

CORNET
Web

CORNET

A user-friendly tool for data mining and integration in Arabidopsis. CORNET…

A user-friendly tool for data mining and integration in Arabidopsis. CORNET allows the browsing of microarray data, the construction of coexpression and protein-protein interaction (PPI) networks and…

CoPIT
Desktop

CoPIT co-interacting protein identification technology

Allows comprehensive identification and analysis of membrane protein…

Allows comprehensive identification and analysis of membrane protein interactomes and their dynamics. CoPIT integrates experimental and computational methods for a coimmunoprecipitation (Co-IP)-based…

JiffyNet
Web

JiffyNet

A public web server specifically designed to instantly construct genome-scale…

A public web server specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a…

MAGI
Desktop

MAGI Merging Affected Genes into Integrated-networks

A computational method that simultaneously integrates protein-protein…

A computational method that simultaneously integrates protein-protein interaction and RNAseq expression profiles during brain development to discover “modules” enriched for de novo mutations in…

InteroPORC
Desktop
Web

InteroPORC

An automatic prediction tool to infer protein-protein interaction networks. It…

An automatic prediction tool to infer protein-protein interaction networks. It is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the…

ANAP
Web

ANAP Arabidopsis Network Analysis Pipeline

Serves to effectively integrate the different data sets and maximize access to…

Serves to effectively integrate the different data sets and maximize access to available data. ANAP has been developed for Arabidopsis protein interaction integration and network-based study to…

TSEMA
Web

TSEMA

A server for efficient mapping assessment. TSEMA calculates an initial mapping…

A server for efficient mapping assessment. TSEMA calculates an initial mapping between two families of proteins based on a Monte Carlo approach and allows the user to interactively modify it based on…

CellWhere
Web

CellWhere

Produces an interactive graphical display that mimics the structure of a cell,…

Produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the…

MyProteinNet
Web

MyProteinNet

Allows users to easily create such context-sensitive protein interaction…

Allows users to easily create such context-sensitive protein interaction networks. Users can automatically gather and consolidate data from up to 11 different databases to create a generic protein…

MEDICI
Desktop

MEDICI Mining Essentiality Data to Identify Critical Interactions

Predicts protein-protein interaction (PPI) essentiality by combining gene…

Predicts protein-protein interaction (PPI) essentiality by combining gene knockdown studies with network models of protein interaction pathways in an analytic framework. MEDICI uses network topology…

PANDA
Desktop

PANDA Preferential Attachment based common Neighbor Distribution derived Associations

Allows the analysis of protein-protein interaction (PPI) networks. PANDA is…

Allows the analysis of protein-protein interaction (PPI) networks. PANDA is designed to perform the following tasks: (1) identify significantly functionally associated protein pairs, (2) predict gene…

Host &ndash…
Dataset

Host &ndash Pathogen Protein Interactions Predicted by Structure

Provides access to interaction prediction datasets for several species. The…

Provides access to interaction prediction datasets for several species. The database contains predictions obtained by applying a computational whole-genome method, to study potential host–pathogen…

ANAT
Desktop

ANAT Advanced Network Analysis Tool

Assists users for inference of functional networks of proteins. ANAT provides…

Assists users for inference of functional networks of proteins. ANAT provides access to interaction data from several sources, advanced algorithms for network reconstruction. It supports four types…

EpiTracer
Desktop

EpiTracer

Find epicenters in condition-specific biological networks, given the…

Find epicenters in condition-specific biological networks, given the protein-protein interaction (PPI) network and gene expression levels. EpiTracer is an algorithm which measures how effectively a…

ATD-Scripts
Desktop

ATD-Scripts

Automates simulations using the Anisotropic Thermal Diffusion (ATD) method.…

Automates simulations using the Anisotropic Thermal Diffusion (ATD) method. ATD-Scripts was constructed by using multiple “contact” definitions encountered in the literature, and developed structural…

MetaPred2CS
Web

MetaPred2CS

A sequence-based meta-predictor specifically designed to predict pairing of the…

A sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming two-component systems (TCSs). MetaPred2CS integrates six…

PPIXpress
Desktop

PPIXpress

A network construction method that exploits expression data at the…

A network construction method that exploits expression data at the transcript-level and thus reveals alterations in protein connectivity not only caused by differential gene expression but also by…

DisVis
Desktop
Web

DisVis

Aims to quantify the information content of intersubunit distance restraints.…

Aims to quantify the information content of intersubunit distance restraints. DisVis employs the concept of accessible interaction space, and the set of all possible complex conformations consistent…

Pepper
Desktop

Pepper Protein complex Expansion using Protein-Protein intERactions

A Cytoscape app designed to identify protein complexes as densely connected…

A Cytoscape app designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. PEPPER resolves connection sub-graph discovery…

Moksiskaan
Desktop

Moksiskaan

A computational platform that can be used to integrate information about the…

A computational platform that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. The database is used to combine…

PrInCE
Desktop

PrInCE Prediction of Interactomes from Co-Elution

Allows analysis of co-fractionation data. PrInCE represents a major conceptual…

Allows analysis of co-fractionation data. PrInCE represents a major conceptual advance over preliminary bioinformatics treatments published by our lab, which provided basic data extraction and curve…

bsl_mtl
Desktop

bsl_mtl Bilinear Sparse Low-rank Multitask Learning

Models interactions between human proteins and three different, but related…

Models interactions between human proteins and three different, but related viruses: Hepatitis C, Ebola virus and Influenza A. bsl_mtl uses a shared low-rank structure in addition to a task-specific…

Profppikernel
Desktop

Profppikernel

An approach to predict PPIs from sequence alone which is based on evolutionary…

An approach to predict PPIs from sequence alone which is based on evolutionary profiles and profile-kernel Support Vector Machines (SVMs). Profppikernel improved significantly over the…

BIANA
Desktop

BIANA Biologic Interaction and Network Analysis

A tool for biological information integration and network management. BIANA is…

A tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological…

PPCheck
Web

PPCheck

Accumulates pseudoenergies to calculate the strength of protein–protein…

Accumulates pseudoenergies to calculate the strength of protein–protein interactions (PPIs). PPCheck can be used to analyze diverse set of protein–protein interfaces. With this method, simple…

PPI-HOG
Desktop

PPI-HOG

Extracts features from protein sequences, using amino acid contact information…

Extracts features from protein sequences, using amino acid contact information to improve prediction accuracy and an ensemble learning method for classification. PPI-HOG is constructed based on…

PredPPIS
Web

PredPPIS Predictor of Protein-Protein Interaction Sites

Predictes the protein–protein interaction (PPIs) sites using only sequence…

Predictes the protein–protein interaction (PPIs) sites using only sequence information. PredPPIS is not dependent on the structural characteristics of protein complexes, it is worth investigating the…

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