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Protein domain prediction software tools | Sequence analysis

Protein domains are subunits that can fold and evolve independently. Identification of domain boundary locations is often the first step in protein folding and function annotations. Most of the current methods deduce domain boundaries by…
G T A T C G C T A
InterProScan
Desktop
Web

InterProScan

Scans sequences against InterPro's signatures. InterProScan allows users…

Scans sequences against InterPro's signatures. InterProScan allows users to characterize a nucleotide or protein function by matching it with models from several different databases and to…

HMMER
Desktop
Web

HMMER

Provides access to the protein homology search algorithms found in the HMMER…

Provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the…

GlobPlot
Web

GlobPlot

A web service that allows the user to plot the tendency within the query…

A web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. GlobPlot successfully identifies inter-domain segments containing linear motifs,…

SANDPUMA
Desktop

SANDPUMA Specificity of AdenylatioN Domain Prediction Using Multiple Algorithms

Assists in prioritization and dereplication of nonribosomal peptide synthetases…

Assists in prioritization and dereplication of nonribosomal peptide synthetases (NRPs) within large datasets. SANDPUMA can prioritize novel scaffolds and analogs within superfamilies of interest…

SWAKK
Web

SWAKK Sliding Window Analysis of Ka and Ks

Detects amino acid or regions under positive selection using a sliding window…

Detects amino acid or regions under positive selection using a sliding window KA/KS analysis. SWAKK is a web application that can perform three features: (i) provides a 3D structures from sequence…

CLADE
Desktop

CLADE CLoser sequences for Annotations Directed by Evolution

Identifies domains in proteins by using all known Pfam domains and the large…

Identifies domains in proteins by using all known Pfam domains and the large quantity of available genomic data spanning through a large panel of species. CLADE is based on a Support Vector Machine…

ThreaDomEx
Web

ThreaDomEx

Predicts structure of continuous domain (CD) and discontinuous domain (DCD).…

Predicts structure of continuous domain (CD) and discontinuous domain (DCD). ThreaDomEx identifies multiple structure templates and then, derives a profile of domain conservation score (DCscore) for…

BacHbpred
Web

BacHbpred

Predicts the corresponding hemoglobin-like (HbL) subclass/family protein for a…

Predicts the corresponding hemoglobin-like (HbL) subclass/family protein for a given amino acid sequence. BacHbpred is based on support vector machines (SVM) modules. It uses amino acid composition…

PKS/NRPS
Web
Desktop

PKS/NRPS

Provides a Hidden Markov Model (HMM) implementation for domain parsing and a…

Provides a Hidden Markov Model (HMM) implementation for domain parsing and a domain substrate prediction. PKS/NRPS is an analysis website were HMM searches are implemented using the software package…

DAMA
Desktop

DAMA Domain Annotation by a Multi-objective Approach

Treats protein domain architecture prediction as a multi-objective optimization…

Treats protein domain architecture prediction as a multi-objective optimization problem. By taking into account known architectural solutions, DAMA identifies them within the protein sequence and…

TreeDom
Web

TreeDom

A web tool for graphically analysing the evolutionary history of domains in…

A web tool for graphically analysing the evolutionary history of domains in multi-domain proteins. Individual domains on the same protein chain may have distinct evolutionary histories, which is…

DoMosaics
Desktop

DoMosaics

An application that unifies protein domain annotation, domain arrangement…

An application that unifies protein domain annotation, domain arrangement analysis and visualization in a single tool. DoMosaics simplifies the analysis of protein families by consolidating disjunct…

CHOP
Desktop

CHOP

Dissects a reasonable fraction proteins into domain-like fragments. CHOP uses…

Dissects a reasonable fraction proteins into domain-like fragments. CHOP uses the minimal coverage of a known domain and the minimal level of sequence similarity. The tool contains three hierarchical…

Porthodom
Desktop

Porthodom

Aims to evaluate the protein similarity based on a cosine distance and a…

Aims to evaluate the protein similarity based on a cosine distance and a maximal weight matching algorithm. Porthodom employs evolutionary information carried by the domain content of proteins and…

Scooby-domain
Desktop
Web

Scooby-domain Sequence hydrophobicity predicts domains

A fast and simple method to identify globular domains in protein sequence,…

A fast and simple method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction…

RNHtool
Desktop

RNHtool

Predicts RNase H domain of retroviruses. RNHtool is a RNH model that annotates…

Predicts RNase H domain of retroviruses. RNHtool is a RNH model that annotates new putative RNHs (np-RNHs) in the retroviruses. It basically predicts RNH domains through recognizing their start and…

CDvist
Web

CDvist

A comprehensive domain visualization tool which combines the best available…

A comprehensive domain visualization tool which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models…

dPUC
Desktop

dPUC domain Prediction Using Context

Improves domain predictions for the genome of the poorly annotated malaria…

Improves domain predictions for the genome of the poorly annotated malaria parasite plasmodium falciparum. dPUC incorporates pairwise context scores between domains, along with traditional domain…

FIEFDom
Desktop

FIEFDom

A method to predict the domain boundaries of a multidomain protein from its…

A method to predict the domain boundaries of a multidomain protein from its amino acid sequence using a fuzzy mean operator. Using the nr-sequence database together with a reference protein set (RPS)…

Fast H-DROP
Web

Fast H-DROP Fast Helical-Domain linker pRediction using OPtimal features

Allows prediction of helical linkers. Fast H-DROP is an accelerated version of…

Allows prediction of helical linkers. Fast H-DROP is an accelerated version of H-DROP, a support vector machine (SVM)-based tool aiming at specifically predicting helical linkers. The software was…

DROP
Desktop
Web

DROP Domain linker pRediction using OPtimal features

A support vector machine (SVM)-based domain linker predictor which was trained…

A support vector machine (SVM)-based domain linker predictor which was trained with 25 optimal features. The optimal combination of features was identified from a set of 3000 features using a random…

DomCut
Web

DomCut

A program to predict inter-domain linker regions solely by amino acid sequence…

A program to predict inter-domain linker regions solely by amino acid sequence information. The prediction is made by using linker index deduced from a data set of domain/linker segments. The linker…

ThreaDom
Desktop
Web

ThreaDom Threading-based Protein Domain Prediction

A template-based algorithm for protein domain boundary prediction. Given a…

A template-based algorithm for protein domain boundary prediction. Given a protein sequence, ThreaDom first threads the target through the PDB library to identify protein template that have similar…

ADDA
Web

ADDA Automatic Domain Decomposition Algorithm

An automatic algorithm for domain decomposition and clustering of all protein…

An automatic algorithm for domain decomposition and clustering of all protein domain families. Alignments derived from an all-on-all sequence comparison are used to define domains within protein…

The Hybrid Method
Web

The Hybrid Method Domain Assignment - The Hybrid Method

A method which recognizes the compact and modular segments of polypeptide…

A method which recognizes the compact and modular segments of polypeptide chains to identify structural domains, and contrast some data sets to illuminate their effect. The Hybrid Method combines…

PPRODO
Desktop

PPRODO Prediction of PROtein DOmain boundaries

Predicts domain boundaries of proteins from sequence information by a neural…

Predicts domain boundaries of proteins from sequence information by a neural network. The network is trained and tested using the values obtained from the PSSM generated by PSI-BLAST. A 10-fold…

HMM-FRAME
Desktop

HMM-FRAME

Classifies protein domains based on an augmented Viterbi algorithm that can…

Classifies protein domains based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. HMM-FRAME corrects sequencing errors and classifies putative…

DoBo
Web

DoBo Domain Boundary

A method to integrate the classification power of machine learning with…

A method to integrate the classification power of machine learning with evolutionary signals embedded in protein families in order to improve protein domain boundary prediction. The method first…

EVEREST
Desktop

EVEREST

An automatic identification and classification of protein domains. EVEREST…

An automatic identification and classification of protein domains. EVEREST combines methodologies from the fields of finite metric spaces, machine learning and statistical modeling and achieves state…

DLP-SVM
Web

DLP-SVM

The prediction of structural domains in novel protein sequences is becoming of…

The prediction of structural domains in novel protein sequences is becoming of practical importance. DLP-SVM is a loop-length-dependent support vector machine (SVM) prediction of domain linkers,…

MSAT
Web

MSAT Modeling and Solvent Accessibility Tool

Allows recognition of solvent exposed hydrophobic residues in a protein…

Allows recognition of solvent exposed hydrophobic residues in a protein sequence. MSAT is able to compare them with those of closely related sequences. It can assist scientist to select the best…

Logol
Desktop

Logol

Permits users to find a pattern in a nucleic or proteic sequence. Logol uses a…

Permits users to find a pattern in a nucleic or proteic sequence. Logol uses a grammar language matching technique to proceed. The user can specify constraints such as position, size, or length. It…

SBASE
Web

SBASE

A project initiated to detect known domain types and predicting domain…

A project initiated to detect known domain types and predicting domain architectures using sequence similarity searching. SBASE uses a curated collection of domain sequences and standard similarity…

DomPred
Web

DomPred

This server provides the user with the results from two completely different…

This server provides the user with the results from two completely different categories of method (DPS and DomSSEA). DomPred can suggest alternative domain predictions, allowing the user to make the…

IS-Dom
Dataset

IS-Dom

A dataset of Independent Structural Domains (ISDs) that are most likely to fold…

A dataset of Independent Structural Domains (ISDs) that are most likely to fold in isolation. IS-Dom was constructed by filtering domains from SCOP, CATH, and DomainParser using quantitative…

DOMpro
Web

DOMpro

A web server to predict protein domain boundaries using 1D-Recursive Neural…

A web server to predict protein domain boundaries using 1D-Recursive Neural Networks and statistical methods. To utilize the evolutionary information encoded in homologous proteins, profiles…

NRPS-PKS
Dataset

NRPS-PKS

Permits comparison of Non-ribosomal peptide synthetases (NRPSs) and polyketide…

Permits comparison of Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) domains. NRPS-PKS is a knowledge-based tool for analysing putative NRPS and PKS gene clusters. It uses…

HMMCAS
Web

HMMCAS

Identifies Cas proteins from a set of protein sequences or a proteome. HMMCAS…

Identifies Cas proteins from a set of protein sequences or a proteome. HMMCAS allows users to find and annotate a collection of Cas protein family Hiden Markov Models (HMMs) for protein sequences or…

PDP-CON
Desktop

PDP-CON

Predicts domain/linker residues in protein chains using a carefully selected…

Predicts domain/linker residues in protein chains using a carefully selected set of physicochemical features. PDP-CON can be useful in functional annotation of complex protein chains, including…

DOMAC
Web

DOMAC

A hybrid domain prediction web service integrating template-based and ab initio…

A hybrid domain prediction web service integrating template-based and ab initio methods. Our hybrid approach uses the template-based method to predict domains for proteins having homologous template…

KemaDom
Web

KemaDom

A domain prediction system by ensembling three kernel machines with the local…

A domain prediction system by ensembling three kernel machines with the local context information among neighboring amino acids. KemaDom, an alternative ab initio predictor, can achieve high…

SSEP-Domain
Web

SSEP-Domain

A protein domain prediction approach which is based on the application of…

A protein domain prediction approach which is based on the application of secondary structure element alignment (SSEA) and profile-profile alignment (PPA) in combination with InterPro pattern…

Meta-DP
Web

Meta-DP

A domain prediction meta-server provides a simple interface to predict domains…

A domain prediction meta-server provides a simple interface to predict domains in a given protein sequence using a number of domain prediction methods. Meta-DP is a convenient resource because…

Armadillo
Desktop

Armadillo

Uses any amino acid index to convert a protein sequence to a smoothed numeric…

Uses any amino acid index to convert a protein sequence to a smoothed numeric profile from which domains and domain boundaries may be predicted. Armadillo provides a simple, but effective method by…

DomHR
Web

DomHR

An accurate predictor of protein domain boundaries based on a creative hinge…

An accurate predictor of protein domain boundaries based on a creative hinge region strategy. A hinge region was defined as a segment of amino acids that covers part of a domain region and a boundary…

DomNet
Desktop

DomNet

A machine learning based domain predictor that can show a more accurate and…

A machine learning based domain predictor that can show a more accurate and stable predictive performance than the existing state-of-the-art models. DomNet is trained using a novel compact domain…

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