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Transmembrane helix detection software tools | Protein structure data analysis

In eukaryotes, all known membrane proteins in the plasma membrane consist of alpha helical transmembrane (TM) bundles connected by loops. Accurate computational prediction of transmembrane helical segments is important for modeling membrane protein…
MEDELLER
Web

MEDELLER

Builds highly reliable core models (which usually correspond to a protein’s…

Builds highly reliable core models (which usually correspond to a protein’s transmembrane (TM) region). Medeller is a method for coordinate generation specialized for membrane proteins (MPs). It…

TMDOCK
Web

TMDOCK

Permits assessment of structural heterogeneity of dimers. TMDOCK is a…

Permits assessment of structural heterogeneity of dimers. TMDOCK is a computational method that models parallel homodimers formed by transmembrane (TM) alpha-helices. This method permits to identify…

AnglerFish
Web

AnglerFish

Provides an easy-to-use webserver for parameterising the angles of…

Provides an easy-to-use webserver for parameterising the angles of transmembrane helices based on Protein Data Bank (PDB) coordinates, with the helical orientations defined by the angles “tilt”…

HELIQUEST
Web

HELIQUEST

Calculates the physicochemical properties and amino acid composition. HELIQUEST…

Calculates the physicochemical properties and amino acid composition. HELIQUEST uses the results to screen any databank in order to identify protein segments possessing similar features. It allows…

TOPCONS
Desktop
Web

TOPCONS

A web server for consensus prediction of membrane protein topology. The…

A web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the…

AmphipaSeek
Web

AmphipaSeek AMPHIPATHIC IN-PLANE MEMBRANE ANCHORS PREDICTION

Predicts in-plane membrane (IPM) anchors. AmphipaSeek is available online on…

Predicts in-plane membrane (IPM) anchors. AmphipaSeek is available online on the NPS@ protein sequence analysis server. This tool uses a method based on a pattern recognition Support Vector Machine…

TMKink
Web

TMKink

Identifies bends from local sequence information. TMKink is a neural network…

Identifies bends from local sequence information. TMKink is a neural network predictor which identifies over two-thirds of all bends. TMKink is a prediction method that provides useful information…

FILM
Desktop

FILM Folding In Lipid Membranes

Generates reasonable models for a number of small transmembrane proteins with…

Generates reasonable models for a number of small transmembrane proteins with both correct chain conformations and topology with respect to the inside– outside polarity of the bilayer. FILM is a…

TMDIM
Web

TMDIM

Calculates energetically favorable oligomerized structures of a pair of…

Calculates energetically favorable oligomerized structures of a pair of transmembrane alpha-helces. TMDIM is a structure modeling application. It analyzes systematically all dimeric conformations…

SheddomeDB
Dataset

SheddomeDB

Integrates publicly available data of the shed membrane proteins. SheddomeDB is…

Integrates publicly available data of the shed membrane proteins. SheddomeDB is a database for the identification of experimentally validated shed membrane protein. It provides numbers of membrane…

MPRAP
Web

MPRAP

Performs both within and outside the membrane regions. MPRAP allows to the user…

Performs both within and outside the membrane regions. MPRAP allows to the user to input amino acid sequences to the server. MPRAP can identify some erroneous protein structures. This tool is able to…

CGDB
Dataset

CGDB

Membrane protein function and stability has been shown to be dependent on the…

Membrane protein function and stability has been shown to be dependent on the lipid environment. CGDB is a database of membrane protein/lipid interactions by coarse-grained molecular dynamics…

MeMotif
Dataset

MeMotif

Collects more than 2000 known and novel computationally predicted linear motifs…

Collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional…

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…

SOSUI
Web

SOSUI

Constructs a system for predicting membrane proteins by an index of amino…

Constructs a system for predicting membrane proteins by an index of amino acids. Amphiphilicity plots of membrane proteins of known 3D structure indicat that this kind of plot is useful in finding…

TMalphaDB
Dataset

TMalphaDB Transmembrane Alpha Helix Database

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

Quantifies the structural distortion induced by a sequence motifs in alpha transmembrane segments. TMalphaDB contains 330 structures of α-helix bundles. To avoid redundancy, only one structure for…

MEMPACK
Desktop

MEMPACK

Creates a transmembrane (TM) topology with optimal helical packing arrangement…

Creates a transmembrane (TM) topology with optimal helical packing arrangement using a force-directed algorithm. The MEMPACK tool can predict the total number of TM helices, their boundaries and…

TopPred
Web

TopPred

A strategy for predicting the topology of bacterial inner membrane proteins is…

A strategy for predicting the topology of bacterial inner membrane proteins is proposed on the basis of hydrophobicity analysis, automatic generation of a set of possible topologies and ranking of…

tmap
Web

tmap

A method for the prediction of protein membrane topology (intra- and…

A method for the prediction of protein membrane topology (intra- and extracellular sidedness) from multiply aligned amino acid sequences after determination of the membrane-spanning segments. The…

TMpred
Web

TMpred

Makes a prediction of membrane-spanning regions and their orientation. The…

Makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins. The…

TMMOD
Web

TMMOD

An improved hidden Markov model for the identification and topology prediction…

An improved hidden Markov model for the identification and topology prediction of transmembrane proteins. Application of TMMOD to a collection of complete genomes shows that the number of predicted…

DAS-TMfilter
Web

DAS-TMfilter

Web-based servers implementing the DAS-TMfilter algorithm have been launched at…

Web-based servers implementing the DAS-TMfilter algorithm have been launched at three mirror sites. The DAS-TMfilter prediction tool takes fasta-format protein queries as input. Each entry starts…

MINNOU
Desktop
Web

MINNOU Membrane protein IdeNtificatioN withOUt

Methods for prediction of alpha-helical as well as beta-sheet transmembrane…

Methods for prediction of alpha-helical as well as beta-sheet transmembrane (TM) domains. This approach is based on a compact representation of an amino acid residue and its environment, which…

TMBB-DB
Dataset

TMBB-DB

This database is a compilation of the predictions made by the Freeman-Wimley…

This database is a compilation of the predictions made by the Freeman-Wimley algorithm, which was shown to be among the most accurate predictor of TMBBs. Also included are N-terminal export signal…

PolyPhobius
Web

PolyPhobius

A general hidden Markov model (HMM) decoding algorithm that combines…

A general hidden Markov model (HMM) decoding algorithm that combines probabilities for sequence features of homologs by considering the average of the posterior label probability of each position in…

HMMTOP
Web

HMMTOP

Predicts both the localization of helical transmembrane segments and the…

Predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins. The user is allowed to submit additional information about segment localization to enhance…

SVMtm
Web

SVMtm

A method developed for prediction of transmembrane helices using support vector…

A method developed for prediction of transmembrane helices using support vector machines. This method can be used to complement current transmembrane helix prediction methods and can be used for…

MemBrain
Web

MemBrain

A method to derive transmembrane inter-helix contacts from amino acid sequences…

A method to derive transmembrane inter-helix contacts from amino acid sequences by combining correlated mutations and multiple machine learning classifiers. Tested on 60 non-redundant polytopic…

PHDhtm
Web

PHDhtm

A neural network system that predicts the locations of helical transmembrane…

A neural network system that predicts the locations of helical transmembrane segments in integral membrane proteins. The prediction method significantly improves on a previous system by using…

MetaTM
Desktop

MetaTM

A consensus method for predicting transmembrane (TM) topologies. MetaTM is…

A consensus method for predicting transmembrane (TM) topologies. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide…

MEMSAT-SVM
Desktop

MEMSAT-SVM

A method capable of automatically identifying pore-lining regions in…

A method capable of automatically identifying pore-lining regions in transmembrane proteins from sequence information alone, which can then be used to determine the pore stoichiometry. MEMSAT-SVM…

TMexpo
Web

TMexpo

A method to predict rotational preferences of transmembrane helices to…

A method to predict rotational preferences of transmembrane helices to facilitate structural modeling. TMexpo first predicts lipid accessibility (the relative accessible surface area in lipid) by…

LIPS
Web

LIPS LIPid-facing Surface

A method for prediction of the transmembrane () helix orientation, which is an…

A method for prediction of the transmembrane () helix orientation, which is an essential step in ab initio modeling of membrane proteins. LIPS is based on a canonical model of the heptad repeat…

MHOLline
Web

MHOLline

Automates protein structure prediction and function annotation. MHOLline…

Automates protein structure prediction and function annotation. MHOLline recognizes and utilizes information of protein sequences including in large-scale genome annotation projects. It is based on…

SOMPNN
Desktop

SOMPNN Self-Organizing Map Probabilistic Neural Network

Predicts the transmembrane helices (TMH). SOMPNN performs prediction with high…

Predicts the transmembrane helices (TMH). SOMPNN performs prediction with high efficiency by exploiting the learning ability of self-organizing map (SOM). It can learn the data distribution knowledge…

CSAH
Web
Desktop

CSAH Charged Single α-Helices

Offers two independent methods for Charged Single α-Helices (CSAH) detection…

Offers two independent methods for Charged Single α-Helices (CSAH) detection in protein sequences. The CSAH server proposes SCAN4CSAH and FT_CHARGE methods. SCAN4CSAH is based on a scoring scheme…

PRED-TMR
Web

PRED-TMR

Predicts transmembrane domains in proteins using solely information contained…

Predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm refines a standard hydrophobicity analysis with a detection of potential…

SCAMPI
Web

SCAMPI

Prediction of membrane protein topology from first principles. SCAMPI allows…

Prediction of membrane protein topology from first principles. SCAMPI allows for requests of up to 100,000 protein sequences, and is appropriate for large benchmark sets and full proteome scans. If…

SOMRuler
Desktop

SOMRuler

A transmembrane helices (TMH) predictor with excellent interpretability. The…

A transmembrane helices (TMH) predictor with excellent interpretability. The SOMRuler uses a self-organizing map (SOM) to learn helices distribution knowledge, which is encoded in the codebook…

CCTOP
Desktop
Web

CCTOP Consensus Constrained TOPology prediction

A web-based application providing transmembrane topology prediction. In…

A web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology…

PONGO
Web

PONGO

A web server that incorporates the state-of-the-art topology predictors in a…

A web server that incorporates the state-of-the-art topology predictors in a single framework, so that putative users can interactively compare and evaluate four predictions simultaneously for a…

ConPred
Web

ConPred

A server for the prediction of transmembrane (TM) topology [i.e. the number of…

A server for the prediction of transmembrane (TM) topology [i.e. the number of TM segments (TMSs), TMS positions and N-tail location] based on a consensus approach by combining the results of several…

TMpro
Web

TMpro

A transmembrane (TM) helix prediction algorithm that uses language processing…

A transmembrane (TM) helix prediction algorithm that uses language processing methodology for TM segment identification. TMpro is primarily based on the analysis of statistical distributions of…

Asymmetric Ez
Web

Asymmetric Ez

A knowledge-based potential for assessing the energies and positions of protein…

A knowledge-based potential for assessing the energies and positions of protein sequences or structures in and on the membrane. The pseudo-energy topological landscapes underscore positional…

WRF-TMH
Web

WRF-TMH

Predicts TM helix segments. In this model, information is extracted from…

Predicts TM helix segments. In this model, information is extracted from membrane protein sequences using compositional index and physicochemical properties. The redundant and irrelevant features are…

THUMBUP
Web

THUMBUP

Topology predictor of transmembrane helical proteins using mean burial…

Topology predictor of transmembrane helical proteins using mean burial propensity Helices in membrane spanning regions are more tightly packed than the helices in soluble proteins. THUMBUP predicts…

TMX
Web

TMX TransMembrane eXposure

Predicts the burial status of transmembrane residues of helical membrane…

Predicts the burial status of transmembrane residues of helical membrane proteins (HMPs). TMX tool yields automatically confidence scores for the prediction made to help users to selectively utilize…

PRIMSIPLR
Web
Desktop

PRIMSIPLR Prediction of Inner-Membrane Situated Pore-Lining Residues

Predicts pore-lining residues (PLR) from the sequences of α-helical…

Predicts pore-lining residues (PLR) from the sequences of α-helical transmembrane proteins. PRIMSIPLR method was developed on a comprehensive data set containing 90 protein structures. The amino…

CNTOP
Desktop

CNTOP

A consensus topology prediction method for alphaTMPs that incorporates four top…

A consensus topology prediction method for alphaTMPs that incorporates four top leading individual topology predictors, and further improves the prediction accuracy by using the predicted…

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