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Other membrane proteins software tools and databases

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…

OPM
Dataset

OPM Orientations of Proteins in Membranes

Provides spatial positions of membrane-bound peptides and proteins of known 3D…

Provides spatial positions of membrane-bound peptides and proteins of known 3D structure in the lipid bilayer. OPM is a curated web resource which contains more than 1200 transmembrane and peripheral…

Membranome
Dataset

Membranome Membrane Proteome

Gathers information about bitopic proteins from six complete genomes (Homo…

Gathers information about bitopic proteins from six complete genomes (Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus…

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…

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.

TOPDOM
Dataset

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…

MEMScore
Web

MEMScore

Allows scoring of membrane protein structures. MEMScore is a web-server…

Allows scoring of membrane protein structures. MEMScore is a web-server implementing a membrane-protein scoring protocol. The software allows the submission of a set of structures, optimizes their…

iCTX-Type
Web

iCTX-Type

Identifies the types of conotoxins in targeting ion channels. iCTX-Type can…

Identifies the types of conotoxins in targeting ion channels. iCTX-Type can become a useful high throughput tool for both basic research and drug development, particularly for in-depth investigation…

CAMPS
Dataset

CAMPS Computational Analysis of the Membrane Protein Space

Provides an automatic classification approach of helical membrane proteins…

Provides an automatic classification approach of helical membrane proteins including at least three transmembrane helices. CAMPS allows users to browse prokaryotic, eukaryotic, and viral genomes. It…

MycoMemSVM
Web

MycoMemSVM

Predicts mycobacterial membrane proteins and their types. MycoMemSVM is an…

Predicts mycobacterial membrane proteins and their types. MycoMemSVM is an online server and a binomial distribution-based feature selection technique able to select over-represented tripeptides. In…

3D-HM
Web

3D-HM The 3D Hydrophobic Moment Vector Calculator

Predicts peptide-bilayer binding geometries. 3D-HM extends the idea of…

Predicts peptide-bilayer binding geometries. 3D-HM extends the idea of molecular hydrophobicity potentials (MHPs), which are based on heuristic or experimental definitions of hydrophobicity for whole…

RBCC
Dataset

RBCC Red Blood Cell Collection

Assists user for identification of membrane protein. RBCC is an interactive…

Assists user for identification of membrane protein. RBCC is an interactive database for detection of red blood cell (RBC) proteins from mass-spectrometry (MS) data sources. This database integrates…

MP:PD
Dataset

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…

GeTFEP
Algorithm

GeTFEP General Transfer Free Energy Profile

Provides a derived method from a non-redundant set of β-barrel transmembrane…

Provides a derived method from a non-redundant set of β-barrel transmembrane proteins (TMBs). GeTFEP reflects the energetic cost of transferring an amino acid side-chain into certain depth of…

TMPL
Dataset

TMPL Transmembrane protein Models Positioned in the Lipid

Provides a database of transmembrane protein models positioned in the lipid…

Provides a database of transmembrane protein models positioned in the lipid bilayer. TMPL is a resource that includes atomistic and coarse-grained protein models oriented in the membrane by ANVIL…

TMB-TFE
Web
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…

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…

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…

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…

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
Dataset

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.

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…

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…

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…

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…

MicRhoDE
Dataset

MicRhoDE

A comprehensive, high-quality and freely accessible database that facilitates…

A comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine…

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…

GPCRsort
Desktop

GPCRsort

Classifies G-protein couple receptor sequences into G Protein-Coupled Receptor…

Classifies G-protein couple receptor sequences into G Protein-Coupled Receptor Data Base (GPCRDB) classes. The database is organized in a hierarchical structure, divided in classes: Rhodopsin like,…

TBBpred
Desktop
Web

TBBpred Transmembrane Beta Barrel prediction

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…

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…

MPEx
Desktop

MPEx Membrane Protein Explorer

Provides a membrane protein explorer. MPEx provides an extendable framework for…

Provides a membrane protein explorer. MPEx provides an extendable framework for physical and biological hydropathy analyses and for b-barrel identification screening. It provides three analysis modes…

MPtopo
Dataset

MPtopo

Provides a resource for the prediction of structure. MPtopo is a database of…

Provides a resource for the prediction of structure. MPtopo is a database of membrane proteins (MPs) and transmembrane (TM) sequences whose topologies have been verified experimentally by means of…

TM Finder
Web

TM Finder

Provides a useful screening operation for identifying their membrane-based…

Provides a useful screening operation for identifying their membrane-based segments. TM Finder is an application that automates and implements the concept of dual threshold hydrophobicity and…

hERGAPDbase
Dataset

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…

KDB
Dataset

KDB

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

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

Mpstruct
Dataset

Mpstruct

Provides access to a list of membrane protein structures.

Provides access to a list of membrane protein structures.

PDBTM
Dataset

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).

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.

TMBETA-GENOME
Dataset

TMBETA-GENOME

Provides annotated b-barrel membrane proteins for completed genomes.…

Provides annotated b-barrel membrane proteins for completed genomes. TMBETA-GENOME includes several features, such as the service for detecting transmembrane b-barrel proteins (TMBs) in genomic…

TMFunction
Dataset

TMFunction

Helps in understanding the relationship between amino acid sequences/structures…

Helps in understanding the relationship between amino acid sequences/structures and functions of membrane proteins. TMFunction is a collection of more than 2900 experimental data about important…

RaftProt
Dataset

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…

PDB_TM
Dataset

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…

nrDB
Dataset

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…

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…

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