Transmembrane proteins play an important role in the living cells for energy production, regulation and metabolism. The fact that half of present-day drugs have some effect on transmembrane proteins (Overington et al., 2006) also underlines their biological importance.

Membrane protein analysis (omic data)

MemType-2L
Web

MemType-2L

Provides a 2-layer predictor. MemType-2L consists of the following steps: the…

Provides a 2-layer predictor. MemType-2L consists of the following steps: the 1st layer prediction engine identifies a query protein as membrane or non-membrane. If it is a membrane protein, the…

OCTOPUS
Web
Desktop

OCTOPUS obtainer of correct topologies for uncharacterized sequences

Predicts transmembrane protein topology. OCTOPUS uses a combination of hidden…

Predicts transmembrane protein topology. OCTOPUS uses a combination of hidden Markov models (HMM) and artificial neural networks. In particular, OCTOPUS fully integrates modeling of…

iMembrane
Web

iMembrane

An homology-based method, which predicts a membrane protein's position…

An homology-based method, which predicts a membrane protein's position within a lipid bilayer. iMembrane is part of Memoir (Membrane protein modelling pipeline). It projects the results of…

EVfold_membrane
Web

EVfold_membrane

Predicts oligomerization, functional sites, and conformational changes in…

Predicts oligomerization, functional sites, and conformational changes in transmembrane proteins. EVfold_membrane applies a maximum entropy approach to infer evolutionary co-variation in pairs of…

TMM@
Web

TMM@ Trans-Membrane alpha-helical Movement Analyzer

Studies the mobility of transmembrane α-helices. TMM@ uses normal mode…

Studies the mobility of transmembrane α-helices. TMM@ uses normal mode analysis (NMA) to characterize the propensity of transmembrane α-helices to be displaced. Starting from a structure file at…

PROFtmb
Desktop

PROFtmb

Predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria.…

Predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. PROFtmb was tested on a representative set of known TMB and non-TMB proteins. It detects 50% of TMBs at 80% accuracy…

mp lipid acc
Web

mp lipid acc

Indentifies lipid accessible residues from the protein structure, implemented…

Indentifies lipid accessible residues from the protein structure, implemented in the RosettaMP framework and available as a webserver. mp_lipid_acc method uses protein structures transformed in…

hERGAPDbase
Data

hERGAPDbase human Ether-a-go-go-Related Gene Action Potential Duration base

A database of electrophysiological experimental data documenting potential…

A database of electrophysiological experimental data documenting potential (human ether-a-go-go-related gene (hERG) channel inhibitory actions and the action potentials duration (APD)-prolongation…

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…

Memoir
Web

Memoir

Produces homology models using alignment and coordinate generation software…

Produces homology models using alignment and coordinate generation software that has been designed specifically for transmembrane proteins. Memoir includes a set of alternative conformations for each…

TOPDOM
Data

TOPDOM

A collection of domains and sequence motifs located conservatively in one side…

A collection of domains and sequence motifs located conservatively in one side of membranes either in transmembrane or globular proteins. TOPDOM was created by predicting the transmembrane status and…

Membranome
Data

Membranome Membrane Proteome

A database for proteome-wide analysis of single-pass membrane proteins.…

A database for proteome-wide analysis of single-pass membrane proteins. Membranome currently collects data on >6000 bitopic proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium…

MP:PD
Data

MP:PD Membrane Protein Packing Database

A comprehensive database of helical membrane proteins featuring internal atomic…

A comprehensive database of helical membrane proteins featuring internal atomic packing densities, internal cavities and internal waters. MP:PD encloses all alpha helical transmembrane proteins…

COMSAT
Web

COMSAT

A hybrid framework for residue contact prediction of transmembrane (TM)…

A hybrid framework for residue contact prediction of transmembrane (TM) proteins, integrating a support vector machine (SVM) method and a mixed integer linear programming (MILP) method. COMSAT…

HMPAS
Web

HMPAS Human Membrane Protein Analysis System

A human membrane protein analysis system containing 36,585 proteins and their…

A human membrane protein analysis system containing 36,585 proteins and their important characteristics. HMPAS integrates known membrane proteins from 19 different publicly available resources. The…

Membrainy
Desktop

Membrainy

A user-friendly, intelligent membrane analysis tool that automatically…

A user-friendly, intelligent membrane analysis tool that automatically interprets a variety of input formats and force fields, is compatible with both single and double bilayers, and capable of…

TBBpred
Desktop
Web

TBBpred

Predicts the transmembrane Beta barrel regions in a given protein sequence. The…

Predicts the transmembrane Beta barrel regions in a given protein sequence. The server uses a forked strategy for predicting residues which are in transmembrane beta barrel regions. Prediction can be…

RaftProt
Data

RaftProt

A database of mammalian lipid raft-associated proteins as reported in…

A database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and…

PPM Server
Web

PPM Server

Calculates rotational and translational positions of transmembrane and…

Calculates rotational and translational positions of transmembrane and peripheral proteins in membranes using their 3D structure (PDB coordinate file) as input. It can be applied to newly determined…

TMPad
Data

TMPad TransMembrane Protein Helix-Packing Database

An integrated repository of experimentally determined structural folds derived…

An integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins.

OPM
Data

OPM Orientations of Proteins in Membranes

A curated web resource that provides spatial positions of membrane-bound…

A curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural…

TMDET
Web

TMDET

It may be used for the detection of the transmembrane regions of membrane…

It may be used for the detection of the transmembrane regions of membrane proteins using their 3D structure only.

KDB
Data

KDB

A Database of Potassium Ion Channel Homology Models & Molecular Dynamics…

A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations.

Mpstruct
Data

Mpstruct

Membrane proteins of known 3d structure.

Membrane proteins of known 3d structure.

SG-MPt_Pred
Web

SG-MPt_Pred

Provides a stacked generalization classifier to predict membrane protein types…

Provides a stacked generalization classifier to predict membrane protein types based on pseudo-amino acid composition. SG-MPt_Pred uses the stacking approach which can combine several types of…

MemHyb-SVM
Web

MemHyb-SVM

Predicts membrane protein types. MemHyb-SVM considers both evolutionary and…

Predicts membrane protein types. MemHyb-SVM considers both evolutionary and physicochemical features. It provides to a classification system based on support vector machine (SVM) with error…

PDB_TM
Data

PDB_TM Protein Data Bank_TM

A collection of transmembrane proteins with known structures automatically…

A collection of transmembrane proteins with known structures automatically updated. PDB_TM is a database using only structural information to locate the most position of the lipid bilayer and to…

TMFoldRec
Desktop

TMFoldRec

A method for fold prediction of membrane segments in transmembrane proteins.…

A method for fold prediction of membrane segments in transmembrane proteins. TMFoldRec based on statistical potentials was tested on a benchmark set containing 124 transmembrane protein (TMP) chains…

nrDB
Data

nrDB

A nonredundant database to compute knowledge-based asymmetric cross-membrane…

A nonredundant database to compute knowledge-based asymmetric cross-membrane potentials from the per-residue distributions of C(beta), C(gamma) and functional group atoms. Hence, focusing on the…

PREDDIMER
Web

PREDDIMER

Reconstructs putative dimer conformations for given sequences of transmembrane…

Reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices.

PDBTM
Data

PDBTM Protein Data Bank of Transmembrane Proteins

Comprehensive and up-to-date transmembrane protein selection of the Protein…

Comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB).

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