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-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…

BioPlex
Dataset

BioPlex

Reflects cellular localization, biological process, and molecular function,…

Reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. BioPlex structure also reveals associations among thousands…

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…

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…

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…

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…

DIIP
Dataset

DIIP Domain-based Isoform Interactome Prediction

Allows users to predict the isoform interactome from an experimentally…

Allows users to predict the isoform interactome from an experimentally determined reference interactome. DIIP permits users to find several informations about human protein-protein interactions…

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…

AraPPINet
Dataset

AraPPINet Arabidopsis Protein-Protein Interaction Network

A genome-wide protein interaction network that is inferred from both…

A genome-wide protein interaction network that is inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574…

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
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…

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…

MauPIR
Dataset

MauPIR Macrotyloma uniflorum Protein Interaction Resource

Predictes protein-protein interactions (PPis) in Horsegram (Kulthi). MauPIR…

Predictes protein-protein interactions (PPis) in Horsegram (Kulthi). MauPIR provides high confidence systems biology information for horsegram genes, proteins and involved processes. Highly reliable…

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…

PreSPI
Desktop

PreSPI Prediction System for Protein Interaction

A probabilistic framework to predict the interaction probability of proteins.…

A probabilistic framework to predict the interaction probability of proteins. We also develop an interaction possibility ranking method for multiple protein pairs. Using the ranking method, one can…

NetworkAnalyst
Web

NetworkAnalyst

A web-based tool designed to perform protein-protein interaction (PPI) network…

A web-based tool designed to perform protein-protein interaction (PPI) network analysis from gene expression data. NetworkAnalyst supports common functions for network topology and module analyses.…

DASMIweb
Web

DASMIweb

Affords the integration, analysis and qualitative assessment of distributed…

Affords the integration, analysis and qualitative assessment of distributed sources of interaction data in a dynamic fashion. Since DASMIweb allows for querying many different resources of protein…

RVM-BiGP-PPI
Web

RVM-BiGP-PPI

A computational method that combines the relevance vector machine (RVM) model…

A computational method that combines the relevance vector machine (RVM) model and Bi‐gram Probabilities (BiGP) for protein-protein interactions (PPIs) detection from protein sequences.…

Multiscale BD algorithm
Algorithm

Multiscale BD algorithm Multiscale Brownian Dynamics simulation algorithm

Enables accelerated computation while capturing the sub-nanometer scale…

Enables accelerated computation while capturing the sub-nanometer scale site-specific interactions of the molecules and their complexes. Multiscale BD algorithm is a computationally efficient…

Tabloid…
Dataset

Tabloid Proteome

Provides unique added value for researchers that are interested in…

Provides unique added value for researchers that are interested in understanding the relations between proteins. Tabloid Proteome is an easily searchable website that presents protein associations…

ComplexViewer
Desktop

ComplexViewer

Allows visualization of molecular interaction data. ComplexViewer offers…

Allows visualization of molecular interaction data. ComplexViewer offers functionality to study hierarchical nesting of complexes and the full range of Proteomics Standards Initiative-Molecular…

OrthoHPI
Dataset

OrthoHPI Orthology–based Host–parasite Protein–protein Interactions

Unravels the host–parasite interactome across 12 human parasites. OrthoHPI is…

Unravels the host–parasite interactome across 12 human parasites. OrthoHPI is based on orthology and its strengths. This tool (1) incorporates high–confidence intra–species interactions, (2)…

ChiPPI
Web

ChiPPI Chimeric Protein–Protein Interactions

Identifies preserved interactors of chimeric proteins. ChiPPI calculates…

Identifies preserved interactors of chimeric proteins. ChiPPI calculates protein-protein interaction (PPI) likelihood by using a domain-domain co-occurrence (DDCOS) score. It is able to evaluate…

PPIDFT
Desktop

PPIDFT Protein-Protein Interaction Discrete Fourier Transformation

Accurately detects protein-protein interaction (PPIs) and reduces false…

Accurately detects protein-protein interaction (PPIs) and reduces false positives. PPIDFT permits to numerically represent protein sequences by biochemical properties of amino acids, which reflect…

PAIRS
Desktop

PAIRS Prediction of Activation/Inhibition Regulation Signaling Pathway

Takes protein interaction pairs as input and gives both known and predicted…

Takes protein interaction pairs as input and gives both known and predicted result of the human protein regulation relationship in terms of activation and inhibition. PAIRS is a method developed to…

apComplex
Desktop

apComplex

Contains functions for estimating protein complex membership using data from…

Contains functions for estimating protein complex membership using data from affinity-purification/mass-spectrometry (AP-MS) experiments. apComplex is essentially a maximal complete subgraph finding…

PyML
Desktop

PyML Python Machine Learning

An interactive object oriented framework for machine learning written in…

An interactive object oriented framework for machine learning written in Python. PyML is a kernel method for predicting protein– protein interactions using a combination of data sources, including…

DIMERO
Web

DIMERO Data Integration for MolEcuar stRucture mOdelling

Allows both the evaluation of interactions between domains as well as a direct…

Allows both the evaluation of interactions between domains as well as a direct access to source data in the form of the PPIs used for the evaluation. In this way, browsing these PPI data offers the…

iRefWeb
Web

iRefWeb

A web interface to protein interaction data consolidated from 10 public…

A web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated…

PAIRPred
Desktop

PAIRPred Partner Aware Interacting Residue PREDictor

Produces predictions using a pre-trained SVM (Support Vector Machine). PAIRpred…

Produces predictions using a pre-trained SVM (Support Vector Machine). PAIRpred generates its prediction for a complex which contains the pairwise interaction scores for each pair of residues from…

Coev2Net
Desktop

Coev2Net

A general framework to predict, assess, and boost confidence in individual…

A general framework to predict, assess, and boost confidence in individual interactions inferred from a high-throughput experiment. The Coev2Net algorithm can be roughly divided into three distinct…

ppiPre
Desktop

ppiPre

Allows user to predict protein-protein interactions (PPI) according to…

Allows user to predict protein-protein interactions (PPI) according to functional and topological similarities. ppiPre calculates similarities between proteins based on their KEGG annotation and PPI…

JET
Desktop

JET Joint Evolutionary Trees

Detects very different types of interactions of a protein with another protein,…

Detects very different types of interactions of a protein with another protein, ligands, DNA, and RNA. JET, based on the Evolutionary Trace (ET) method, introduces a novel way to treat evolutionary…

Prr-BS
Desktop

Prr-BS

Identifies the binding sites by finding two complementary 3D substructures,…

Identifies the binding sites by finding two complementary 3D substructures, where each substructure from one protein. Prr-BS is a method for predicting protein-protein binding sites in complexes.…

MultiTF-PPI
Desktop

MultiTF-PPI

Contains the source Matlab codes for the transcription factor binding site…

Contains the source Matlab codes for the transcription factor binding site (TFBS) predictors MultiTF and MultiTF-PPI with two different priors. MultiTF-PPI is a probabilistic protein-protein…

PPISearch
Web

PPISearch Protein-Protein Interaction Search

Identifies homologous protein-protein interactions (PPIs) (called PPI family)…

Identifies homologous protein-protein interactions (PPIs) (called PPI family) and infers transferability of interacting domains and functions of a query protein pair. PPISearch first identifies two…

BIPS
Web

BIPS Biologic Interactions and Network Analysis Interolog Prediction Server

Offers a web-based interface to facilitate PPI predictions based on interolog…

Offers a web-based interface to facilitate PPI predictions based on interolog information. BIPS benefits from the capabilities of the framework BIANA to integrate the several PPI-related databases.…

EnPPIpred
Web

EnPPIpred Enteropathogen Protein Protein Interactions Prediction

A web server that predicts intra protein protein interaction of entheropathogen…

A web server that predicts intra protein protein interaction of entheropathogen including Escherichia coli (E. coli), Salmonella Typhi, Shigella flexneri, Vibrio cholerae & Yersinia…

SCOWLP
Web

SCOWLP

The main purpose of this server is to allow individual and comparative analysis…

The main purpose of this server is to allow individual and comparative analysis of protein interactions. The user can easily navigate through the classification till the family of interest, where all…

modPDZpep
Web

modPDZpep

Allows prediction of interaction partners of human PDZ domains. modPDZpep is a…

Allows prediction of interaction partners of human PDZ domains. modPDZpep is a web application providing an online interface for structural analysis of modeled PDZ peptide complexes. It uses…

PPI_RF
Web

PPI_RF

A method based on the random forests algorithm and discrete wavelet transform…

A method based on the random forests algorithm and discrete wavelet transform to timely predict protein-protein-interactions. The pipeline of PPI_RF is composed of three main steps: i) the protein…

SPPS
Web

SPPS Sequence-based Protein Partners Search

A web-based tool "Sequence-based Protein Partners Search" (SPPS) to…

A web-based tool "Sequence-based Protein Partners Search" (SPPS) to explore interacting partners of proteins, by searching over a large repertoire of proteins across many species. SPPS…

dnet
Desktop

dnet

An open-source R package for omics data integrative analysis in terms of…

An open-source R package for omics data integrative analysis in terms of network, evolution and ontology. These functions are used for network analysis and visualisation, including: identification of…

PiNAT
Desktop

PiNAT Protein interaction Network Assessment Tool

Generates protein-protein interaction (PPI) networks around proteins of…

Generates protein-protein interaction (PPI) networks around proteins of interest. PiNAT is an automated system that offers a framework for combining the micro-level analysis of individual molecules…

Mirin
Web

Mirin MicroRNA Regulatory Modules in Protein-Protein Interaction Network

An online tool for identification of micorRNA-mediated module which is formed…

An online tool for identification of micorRNA-mediated module which is formed by protein-protein interactions (PPIs). Mirin integrates microRNA regulations and PPIs with microRNA/mRNA expression data…

SpirPro
Web

SpirPro

An analysis platform containing an integrated proteome and PPI database that…

An analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro…

iPPI-Esml
Web

iPPI-Esml

An ensemble classifier for identifying the interactions of proteins. In the PPI…

An ensemble classifier for identifying the interactions of proteins. In the PPI predictor, a protein pair is formulated by a general form of PseAAC whose components are defined via the following…

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…

ProDGe
Web
Desktop

ProDGe Protein Domain Gene

Visualizes existing and suggests novel domain-domain interactions and…

Visualizes existing and suggests novel domain-domain interactions and protein-protein interactions (PPI) at the domain level. Based on known domain interactions, ProDGe suggests novel protein…

STRINGdb
Desktop

STRINGdb Search Tool for the Retrieval of Interacting proteins database

Provides an R interface to the STRING protein-protein interactions (PPI)…

Provides an R interface to the STRING protein-protein interactions (PPI) database. STRINGdb offers functions that take in input a data frame containing as logFC column that reports the logarithm of…

pISTil
Desktop
Wormpath
Web

Wormpath

A software tool for molecular network discovery which operates on the genetic…

A software tool for molecular network discovery which operates on the genetic and physical interaction data of the Wormbase, a comprehensive resource of molecular data on Caenorhabditis elegans.…

SAPIN
Web

SAPIN Structural Analysis of Protein Interaction Networks

A framework dedicated to the structural analysis of protein interaction…

A framework dedicated to the structural analysis of protein interaction networks. SAPIN first identifies the protein parts that could be involved in the interaction and provides template structures.…

iLoops
Web

iLoops

A web server that predicts whether a pair of proteins can interact using local…

A web server that predicts whether a pair of proteins can interact using local structural features. The inputs of the server are as follows: (i) the sequences of the query proteins and (ii) the pairs…

HIVsemi
Desktop

HIVsemi

A semi-supervised multi-task framework for predicting PPIs from not only…

A semi-supervised multi-task framework for predicting PPIs from not only labeled, but also partially labeled reference sets. The basic idea is to perform multi-task learning on a supervised…

DHAC
Desktop

DHAC Dynamical Hierarchical Agglomerative Clustering

A method for clustering time-evolving networks. With link prediction as an…

A method for clustering time-evolving networks. With link prediction as an objective assessment metric, DHAC provides a substantial advance over existing clustering methods.

POINeT
Web

POINeT

An integrated web service to simplify the process of protein-protein…

An integrated web service to simplify the process of protein-protein interaction (PPI) searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple…

iWRAP
Desktop

iWRAP Interface Weighted RAPtor

A threading-based method to predict protein interaction from protein sequences.…

A threading-based method to predict protein interaction from protein sequences. iWRAP predicts whether two proteins interact by combining a novel linear programming approach for interface alignment…

BindML
Web
Desktop

BindML

Predicts protein-protein interaction (PPI) sites using phylogenetic…

Predicts protein-protein interaction (PPI) sites using phylogenetic substitution models. BindML tries to score and identify surface residues of a protein data bank (PDB) structure which exhibits…

OntoNorm
Desktop

OntoNorm

An open source machine learning framework to automatically map concepts in an…

An open source machine learning framework to automatically map concepts in an ontology to text. OntoNorm maps the protein-protein interaction (PPI) relevant articles with corresponding interaction…

PIPE
Web

PIPE Protein-protein Interaction Prediction Engine

This tool is capable of predicting protein-protein interactions for any target…

This tool is capable of predicting protein-protein interactions for any target pair of the yeast Saccharomyces cerevisiae proteins from their primary structure and without the need for any additional…

ppiTrim
Desktop

ppiTrim

Assists users in constructing non-redundant, consistently annotated and…

Assists users in constructing non-redundant, consistently annotated and up-to-date reference data sets. ppiTrim is a script that processes iRefIndex and produces a consolidated data set of physical…

KegHier
Desktop

KegHier

Handles specially formatted text files, called hierarchical text files. KegHier…

Handles specially formatted text files, called hierarchical text files. KegHier is a standalone Java application for browsing and searching functional hierarchies in KEGG BRITE. The default files are…

ProPrInt
Desktop
Web

ProPrInt Protein-Protein Interaction Predictor

Support Vector Machine (SVM) based models have been developed for…

Support Vector Machine (SVM) based models have been developed for discriminating interacting and non-interacting pairs of proteins from their amino acid sequence. ProPrInt predicts physical or…

PPInterFinder
Web

PPInterFinder

A web-based text mining tool to extract human PPIs from biomedical literature.…

A web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE…

MiMI
Web

MiMI Michigan Molecular Interactions

Molecular interaction data exists in a number of repositories, each with its…

Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. MiMI assists scientists searching through this profusion of…

PsePSSM
Web

PsePSSM Pseudo Position-Specific Score Matrix

Predicts protein-protein interactions (PPIs) using the Rotation Forest (RF)…

Predicts protein-protein interactions (PPIs) using the Rotation Forest (RF) combine with Pseudo Position-Specific Score Matrix (PPSSM). PsePSSM is a sequence-based computational method for predicting…

pSTIING
Web

pSTIING

A publicly accessible web-based application and knowledgebase featuring 65 228…

A publicly accessible web-based application and knowledgebase featuring 65 228 distinct molecular associations (comprising protein-protein, protein-lipid, protein-small molecule interactions and…

PICI
Web

PICI Protein Inter-Chain Interaction

Identifies protein inter-chain interaction (PICI) sites and various…

Identifies protein inter-chain interaction (PICI) sites and various interactions that contribute to the specificity and strength of the protein complex. PICI identifies and calculates the…

DCTRF
Web

DCTRF

Combines protein evolutionary information. DCTRF is a sequence-based approach…

Combines protein evolutionary information. DCTRF is a sequence-based approach for predicting Protein-Protein Interactions (PPIs) with Position-Specific Scoring Matrix (PSSM) and Discrete Cosine…

RVMAB-PPI
Web

RVMAB-PPI

A computational method that combines the Relevance Vector Machine (RVM) model…

A computational method that combines the Relevance Vector Machine (RVM) model and Average Blocks (AB) to predict protein-protein interactions (PPIs) from protein sequences. RVMAB-PPI main…

InterSPPI
Web
Desktop

InterSPPI Inter-Species Protein–Protein Interaction predictor

Allows prediction of plant–pathogen protein–protein interaction. InterSPPI…

Allows prediction of plant–pathogen protein–protein interaction. InterSPPI is a webserver, implementing a Random Forest (RF)-based method, that was developed to predict Arabidopsis–pathogen…

goCCA
Desktop

goCCA

A statistical framework that is built upon canonical correlation analysis.…

A statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in protein-protein interaction network (PINs) and Gene…

Prediction of…
Desktop

Prediction of protein-protein interaction

Predictes protein-protein interactions (PPIs) using primary sequences of two…

Predictes protein-protein interactions (PPIs) using primary sequences of two proteins. The prediction model is constructed based on Random Forest and ensemble feature representation scheme. In…

Ulysses
Web

Ulysses

A user-oriented system that uses a process called Interolog Analysis for the…

A user-oriented system that uses a process called Interolog Analysis for the parallel analysis and display of protein interactions detected in various species. Ulysses was designed to perform such…

hF-measure
Desktop

hF-measure

Takes into account the hierarchical organization of protein function…

Takes into account the hierarchical organization of protein function annotations. hF-measure can be used to identify clusters based on function annotations and function similarity. It can evaluate a…

ModuleRole
Desktop
Web

ModuleRole

A user-friendly web server tool which finds modules in PPI network and defines…

A user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes…

InPrePPI
Web
Desktop

InPrePPI Integration method for Prediction of Protein-Protein Interactions

A web-based application for the prediction of protein-protein interactions…

A web-based application for the prediction of protein-protein interactions (PPIs) using one of the four genomic context based methods (phylogenetic profile method, gene cluster method, gene fusion…

Information