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Transmembrane (TM) beta barrel detection software tools | Protein structure data analysis

β-Barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They are important for pore formation, membrane anchoring, and enzyme activity. These proteins are also often responsible for…
partiFold TMB
Web
Desktop

partiFold TMB

Investigates the folding landscape of TMBs (transmembrane b-barrels). PartiFold…

Investigates the folding landscape of TMBs (transmembrane b-barrels). PartiFold TMB estimates inter-beta-strand residue interaction probabilities and foresees contacts and per-residue X-ray crystal…

TOBMODEL
Web

TOBMODEL

Predicts a large set of alternative topologies for a protein. TOBMODEL is an…

Predicts a large set of alternative topologies for a protein. TOBMODEL is an online pipeline appropriate for 3D model generation of putative transmembrane beta barrel proteins. It obtains predicted…

BetaTop
Desktop

BetaTop

Searches the conformational space of a protein to predict its β-sheet…

Searches the conformational space of a protein to predict its β-sheet structure. BetaTop is a method which deals with the proteins with higher number of β-strands. This method has many advantages:…

BOMP
Web

BOMP Beta-barrel Outer Membrane protein Predictor

A program that predicts whether or not a polypeptide sequence from a…

A program that predicts whether or not a polypeptide sequence from a Gram-negative bacterium is an integral beta-barrel outer membrane protein. BOMP is based on two separate components to recognize…

PredαTM and PredβTM
Web

PredαTM and PredβTM Transmembrane Region Predictors

Two independent algorithms, which predict the transmembrane regions of integral…

Two independent algorithms, which predict the transmembrane regions of integral membrane proteins. PredαTM and PredβTM predict respectively the probable alpha helical transmembrane regions and the…

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…

PRED-TMBB
Web

PRED-TMBB

A web server which is capable of predicting the transmembrane strands and the…

A web server which is capable of predicting the transmembrane strands and the topology of beta-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model,…

TMB-Hunt
Web

TMB-Hunt TransMembrane Barrel-Hunt

A program that uses a modified k-nearest neighbour (k-NN) algorithm to classify…

A program that uses a modified k-nearest neighbour (k-NN) algorithm to classify protein sequences as transmembrane beta-barrel (TMB) or non-TMB on the basis of whole sequence amino acid composition.…

TMbetaDB
Dataset

TMbetaDB Transmembrane Beta Sheet Database

Quantifies the structural distortion induced by a sequence motifs in beta…

Quantifies the structural distortion induced by a sequence motifs in beta transmembrane segments. TMbetaDB contains 107 structures of β-barrels. To avoid redundancy, only one structure for each…

MCMBB
Web

MCMBB Markov Chain Model for Beta Barrels

Discriminates beta-barrel outer membrane proteins from globular proteins and…

Discriminates beta-barrel outer membrane proteins from globular proteins and from alpha-helical membrane proteins. The algorithm is based on a 1st order Markov Chain model, which captures the…

BOCTOPUS
Web

BOCTOPUS

An improved method for the topology prediction of transmembrane beta barrel…

An improved method for the topology prediction of transmembrane beta barrel proteins (TMBs) by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and…

BetAware
Web
Desktop

BetAware

Detects TransMembrane β-Barrel (TMBB) and predicts topology in prokaryotes.…

Detects TransMembrane β-Barrel (TMBB) and predicts topology in prokaryotes. BetAware allows both prediction steps based on advanced machine-learning methods. For TMBB detection, BetAware exploits a…

BETApro
Web
Desktop

BETApro

A modular approach to the problem of predicting/assembling protein β-sheets in…

A modular approach to the problem of predicting/assembling protein β-sheets in a chain. BETApro provides an integrated prediction of β-sheet architectures by predicting β-strand pairs, β-strand…

TMBpro
Web

TMBpro

A suite (TMBpro) of specialized predictors for predicting secondary structure…

A suite (TMBpro) of specialized predictors for predicting secondary structure (TMBpro-SS), beta-contacts (TMBpro-CON) and tertiary structure (TMBpro-3D) of transmembrane beta-barrel proteins. Working…

ConBBPRED
Web

ConBBPRED

Different available methods for topology prediction of beta-barrel outer…

Different available methods for topology prediction of beta-barrel outer membrane proteins are compared. The consensus prediction method optimizes the predicted topology with a dynamic programming…

transFold
Web

transFold

A software tool and web interface for the tmmtsag algorithm. transFold is an…

A software tool and web interface for the tmmtsag algorithm. transFold is an application of multi-tape S-attribute grammars for the prediction of β transmembrane protein supersecondary structure.

TMBETA-NET
Web

TMBETA-NET

A web-server for discriminating outer membrane proteins and predicting their…

A web-server for discriminating outer membrane proteins and predicting their membrane spanning beta-strand segments. The amino acid compositions of globular and outer membrane proteins have been…

BTMX
Web

BTMX Beta barrel TransMembrane eXposure

Predicts the structural topology of transmembrane beta barrels (TMBs) by…

Predicts the structural topology of transmembrane beta barrels (TMBs) by employing only the frequency profile of the amino acids in a given sequence. BTMX is a computational method based on a hidden…

TMB-KNN
Web

TMB-KNN

A k-nearest neighbor (K-NN) method for discriminating transmembrane beta-barrel…

A k-nearest neighbor (K-NN) method for discriminating transmembrane beta-barrel (TMB) and non-TMB proteins. We start with a method that makes predictions based on a distance computed from residue…

TMBETADISC-RBF
Web

TMBETADISC-RBF

Discriminating outer membrane proteins (OMPs) from other folding types of…

Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important task both for identifying OMPs from genomic sequences and for the successful…

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