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Protein-protein interaction site detection software tools | Protein structure data analysis

The identification of protein-protein interaction sites is an essential intermediate step for mutant design and the prediction of protein networks. In recent years a significant number of methods have been developed to predict these interface…
PRISM
Web

PRISM Protein Interactions By Structural Matching

Enables fast and accurate prediction of protein-protein interactions (PPIs).…

Enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation…

JET2 Viewer
Dataset

JET2 Viewer

A database of predicted multiple, possibly overlapping, protein-protein…

A database of predicted multiple, possibly overlapping, protein-protein interaction (PPI). JET2 Viewer reports putative protein binding sites for all three-dimensional (3D) structures available in…

RF PPI
Desktop

RF PPI Random Forest Protein-Protein Interaction

Captures the common properties of both homodimer and heterodimer interfaces. RF…

Captures the common properties of both homodimer and heterodimer interfaces. RF PPI contains the backbone flexibility score predicted by DynaMine which is the first direct predictor of dynamics from…

Probe
Desktop

Probe

Allows users to evaluate atomic packing, within or between molecules. Probe…

Allows users to evaluate atomic packing, within or between molecules. Probe implements the contact dot algorithm, which uses a very small probe and leaves a dot when the probe does touch another…

3DIANA
Web
Desktop

3DIANA 3D Domain Interaction Analysis

A web based environment designed to integrate bioinformatics-like information…

A web based environment designed to integrate bioinformatics-like information for the analysis of protein interactions and quaternary structure modellling. 3DIANA is specially targeted to the cases…

SeRenDIP
Web
Desktop

SeRenDIP

Predicts homomeric and heteromeric protein-protein interaction (PPI) sites.…

Predicts homomeric and heteromeric protein-protein interaction (PPI) sites. SeRenDIP can capture the common properties of both homodimer and heterodimer interfaces. It was trained using homodimer…

MFPred
Desktop

MFPred Mean-Field theory-based Prediction

Expresses specificity as a sitewise probability distribution function for…

Expresses specificity as a sitewise probability distribution function for protein-peptide interfaces. MFPred can obtain multi-specificity predictions for diverse classes of protein-recognition…

DynaFace
Web

DynaFace

Exploits the dynamics of protein complexes in order to detect obligatory vs.…

Exploits the dynamics of protein complexes in order to detect obligatory vs. non-obligatory interactions among the subunits. The global perspective of interactions across the subunits interface is…

iFrag
Web

iFrag

Infers possible interacting regions between two proteins by searching minimal…

Infers possible interacting regions between two proteins by searching minimal common sequence-fragments of the interacting protein pairs. iFrag is a sequence-based computational method that derives a…

INTBuilder
Desktop

INTBuilder INTerface Builder

Reads the output of rigid-body docking software. INTBuilder detects…

Reads the output of rigid-body docking software. INTBuilder detects protein-protein interfaces. It can identify the binding sites of small molecules, such as chemical compounds, from conformations…

DXEC-RF
Web

DXEC-RF

Allows to predict protein-protein interactions (PPIs). DXEC-RF incorporates six…

Allows to predict protein-protein interactions (PPIs). DXEC-RF incorporates six coding methods and a feature selection method to construct a classifier. It was trained on a yeast/human protein…

webPIPSA
Web

webPIPSA Protein Interaction Property Similarity Analysis

Permits the classification of proteins according to their interaction…

Permits the classification of proteins according to their interaction properties. webPIPSA is a web server that enables the use of Protein Interaction Property Similarity Analysis (PIPSA) to compare…

PDBparam
Web

PDBparam

Computes more than 50 structure-based features for any given protein structure.…

Computes more than 50 structure-based features for any given protein structure. PDBparam can deal with inter residue interactions, amino acid propensities, physicochemical properties, and binding…

InterPred
Desktop

InterPred

Predicts and models protein protein interactions (PPIs) from sequence using…

Predicts and models protein protein interactions (PPIs) from sequence using structural modeling combined with massive structural comparisons and molecular docking. Starting from two protein…

eRankPPI
Desktop

eRankPPI

Employs a series of attributes to re-rank docking conformations, including…

Employs a series of attributes to re-rank docking conformations, including residue-level interface probabilities, protein docking contact potentials, and energy-based scores. eRankPPI is an algorithm…

ContPro
Web

ContPro

Calculates amino acid contact distances in proteins at different distance…

Calculates amino acid contact distances in proteins at different distance threshold from the 3 Dimensional (3D)-structure of the protein. ContPro calculates the distance between selected protein…

PredUs
Web

PredUs

A flexible, interactive, template-based webserver to predict protein-protein…

A flexible, interactive, template-based webserver to predict protein-protein interface of a given monomeric query protein using its close and remote structural neighbors. Potential interfacial…

toolbx_pdb
Desktop

toolbx_pdb

Allows users to manipulate or modify tasks on a protein complex ensemble.…

Allows users to manipulate or modify tasks on a protein complex ensemble. toolbx_pdb assists users in identification of protein interactions. This tool can setup, monitor and analyze a virtual…

IntPred
Desktop

IntPred

Detects protein-protein interaction (PPI) sites. IntPred uses sequence and…

Detects protein-protein interaction (PPI) sites. IntPred uses sequence and structure information to create features. It returns a prediction label at either the surface patch- or residue-level. It is…

CIPS
Desktop

CIPS Combined Interface Propensity for decoy Scoring

Provides a method able to add constraints to the degrees of freedom of the…

Provides a method able to add constraints to the degrees of freedom of the quaternary structure. CIPS is a valuable method for systematically screening the large amount of poses returned by…

SpotOn
Web

SpotOn

Enables accurate identification of binding Hot-Spots in protein-protein…

Enables accurate identification of binding Hot-Spots in protein-protein complexes with minimal input requirements. SpotOn is an easy to use and publicly accessible web server that helps to classify…

ISPRED4
Web

ISPRED4

Predicts protein-protein interaction (PPI) sites on unbound monomer surfaces in…

Predicts protein-protein interaction (PPI) sites on unbound monomer surfaces in the absence of interaction partners. ISPRED4 exploits a richer set of 46 features derived from both sequence and…

DeepPPI
Desktop

DeepPPI Deep neural networks for Protein-Protein Interactions

Learns the representations of proteins pairs. DeepPPI extracts high-level…

Learns the representations of proteins pairs. DeepPPI extracts high-level discriminative features from common protein descriptors. It is based on a layer-wise abstraction method which permits to give…

Multi-VORFFIP
Web

Multi-VORFFIP

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding…

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding sites. Multi-VORFFIP utilizes a wide range of structural, evolutionary, experimental and energy-based information that…

iPPBS-Opt
Web

iPPBS-Opt

A sequence-based ensemble classifier for identifying protein-protein binding…

A sequence-based ensemble classifier for identifying protein-protein binding sites by optimizing imbalanced training datasets. We have used: (1) the K-Nearest Neighbors Cleaning (KNNC) and Inserting…

iPPBS-PseAAC
Web

iPPBS-PseAAC

Identifies protein-protein binding sites by incorporating the physicochemical…

Identifies protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition. Cross-validation tests indicate that…

SPR
Desktop

SPR Single domain based Patch Recognition

Allows to analyze protein-protein through an interactive interface. SPR is an…

Allows to analyze protein-protein through an interactive interface. SPR is an interface residue recognition method based on the quantitative residue interface propensity index (QIPI). This method is…

BindProf
Web

BindProf

A method for predicting free energy changes (ΔΔG) of protein-protein binding…

A method for predicting free energy changes (ΔΔG) of protein-protein binding interactions upon mutations of residues at the interface. BindProf is an interface binding profile score, formed from an…

ProMateus
Web

ProMateus

Allows you to suggest a new feature that might improve the prediction of the…

Allows you to suggest a new feature that might improve the prediction of the binding site location. This transforms the individual research into a community exercise, bringing out the best from all…

CRF-PPI
Desktop

CRF-PPI

A sequence-based protein-protein interaction (PPI) site predictor which takes…

A sequence-based protein-protein interaction (PPI) site predictor which takes the combined features of position-specific scoring matrices, averaged cumulative hydropathy, and predicted relative…

eFindSitePPI
Desktop
Web

eFindSitePPI

Detects protein binding sites and residues using meta-threading. eFindSitePPI…

Detects protein binding sites and residues using meta-threading. eFindSitePPI also predicts interfacial geometry and specific interactions stabilizing protein-protein complexes, such as hydrogen…

meta-PPISP
Web

meta-PPISP

A meta web server built on three individual web servers: cons-PPISP, PINUP, and…

A meta web server built on three individual web servers: cons-PPISP, PINUP, and Promate. A linear regression method, using the raw scores of the three severs as input, was trained on a set of 35…

InterProSurf
Web

InterProSurf

Predicts interacting amino acid residues in proteins that are most likely to…

Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on…

PSIVER
Web

PSIVER

A server for the prediction of protein-protein interaction sites in protein…

A server for the prediction of protein-protein interaction sites in protein sequences. Only sequence features (position-specific scoring matrix and predicted accessibility) are used for training a…

BSpred
Desktop
Web

BSpred

A neural network based algorithm for predicting binding site of proteins from…

A neural network based algorithm for predicting binding site of proteins from amino acid sequences. BSpred was extensively trained on the sequence-based features including protein sequence profile,…

SPRINGS
Desktop

SPRINGS Sequence-based predictor of PRotein-protein interactING Sites

A computational approach using artificial neural networks for predicting…

A computational approach using artificial neural networks for predicting protein-protein interaction sites based on evolutionary conservation, averaged cumulative hydropathy and predicted relative…

ProMate
Web

ProMate

A program that predicts potential protein-protein binding sites for a given…

A program that predicts potential protein-protein binding sites for a given unbound protein. The ability to predict the location of protein-protein interfaces has far reaching implications both…

CPORT
Web

CPORT Consensus Prediction Of interface Residues in Transient complexes

An algorithm for the prediction of protein-protein interface residues. CPORT…

An algorithm for the prediction of protein-protein interface residues. CPORT combines six interface prediction methods into a consensus predictor. CPORT predictions can be used as active and passive…

PIER
Web

PIER Protein IntErface Recognition

A method for predicting interfaces from a single protein structure that is…

A method for predicting interfaces from a single protein structure that is based on local statistical properties of the protein surface derived at the level of atomic groups. The accuracy,…

WHISCY
Web

WHISCY

A program to predict protein-protein interfaces. WHISCY is primarily based on…

A program to predict protein-protein interfaces. WHISCY is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a…

cons-PPISP
Web

cons-PPISP consensus Protein-Protein Interaction Site Predictor

A consensus neural network method for predicting protein-protein interaction…

A consensus neural network method for predicting protein-protein interaction sites. Given the structure of a protein, cons-PPISP will predict the residues that will likely form the binding site for…

PresCont
Desktop

PresCont

Predicts in a robust manner amino acids that constitute protein-protein…

Predicts in a robust manner amino acids that constitute protein-protein interfaces (PPIs). PresCont reaches state-of-the-art classification quality on the basis of only four residue properties that…

SPPIDER
Web
PIPE-Sites
Web

PIPE-Sites

A method of protein specific binding site prediction based on pairs of…

A method of protein specific binding site prediction based on pairs of re-occurring polypeptide sequences, which have been previously shown to accurately predict protein-protein interactions.…

NPS-HomPPI
Web

NPS-HomPPI Non partner-specific HomPPI

A sequence homology-based method for predicting protein-protein interface…

A sequence homology-based method for predicting protein-protein interface residues. NPS-HomPPI can be used to predict interface residues of a query protein in the absence of knowledge of the…

PS-HomPPI
Web

PS-HomPPI Partner-specific HomPPI

A sequence-based partner-specific protein-protein interface residue prediction…

A sequence-based partner-specific protein-protein interface residue prediction server. Given two potential interacting protein sequences, PS-HomPPI predicts the interface residues between these two…

VORFFIP
Web

VORFFIP Voronoi Random Forest Feedback Interface Predictor

A structure-based computational method for prediction of protein binding sites.…

A structure-based computational method for prediction of protein binding sites. VORFFIP makes use of broad set of heterogeneous data and defined of residue environment, by means of Voronoi Diagrams…

PrISE
Web

PrISE Prediction of protein-protein Interface residues using Structural Elements

Predicts interface residues using local surface structural similarity. PrISe…

Predicts interface residues using local surface structural similarity. PrISe represents a local surface structure using structural elements. A structural element represents the surface of a central…

PSAIA
Desktop

PSAIA Protein Structure and Interaction Analyzer

Computes geometric parameters for large sets of protein structures in order to…

Computes geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction (PPI) sites. PSAIA offers a PIADA (Protein Interaction Atom Distance…

DOMprint
Web

DOMprint

Provides a domain-domain interaction (DDI) prediction server. Domprint is a web…

Provides a domain-domain interaction (DDI) prediction server. Domprint is a web app that incorporates different modules to: (i) predict whether two domain interacts with each other or not, given a…

ProtInDb
Dataset

ProtInDb PROTein-protein INterface residues Data Base

Allows to visualize amino acid residues belonging to the interface between…

Allows to visualize amino acid residues belonging to the interface between proteins chains and to construct data sets of protein-protein interface residues (IR). ProtInDb stores protein-protein IR…

ProtrWeb
Web
Desktop

ProtrWeb

Calculates various commonly used structural and physicochemical descriptors and…

Calculates various commonly used structural and physicochemical descriptors and proteochemometrics modeling descriptors for amino acid sequences. Users can select appropriate descriptors calculated…

CaMELS
Web

CaMELS CalModulin intEraction Learning System

Allows biologists to working on analyzing the functions and interaction…

Allows biologists to working on analyzing the functions and interaction behavior of CaM (Calmodulin) and its target proteins. CaMELS uses protein sequence information only and offers state of the art…

RVMBIGP
Web

RVMBIGP

Predicts self-interacting proteins (SIPs) based on protein amino acids…

Predicts self-interacting proteins (SIPs) based on protein amino acids sequence. RVMBIGP is based on the Relevance Vector Machine (RVM) model combined with Bi-gram probability (BIGP). It can…

LocFuse
Desktop

LocFuse

An ensemble learning method which is useful in human protein–protein…

An ensemble learning method which is useful in human protein–protein interaction (PPI) prediction. LocFuse uses eight different genomic and proteomic features along with four types of different…

The…
Desktop

The Interactorium

A tool in which a Virtual Cell is used as the context for the seamless…

A tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The Interactorium has been…

PPIevo
Desktop

PPIevo

An evolutionary based feature extraction algorithm for protein-protein…

An evolutionary based feature extraction algorithm for protein-protein interaction (PPI) prediction. PPIevo extracts the evolutionary feature from position-specific scoring matrix (PSSM) of protein…

metaPIS
Web

metaPIS

Predicts interaction sites based on protein sequences by integrating five…

Predicts interaction sites based on protein sequences by integrating five different algorithms employing meta-method, Majority Vote and SVMhmm Regression techniques. The 'metaPIS'…

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