1 - 21 of 21 results

TransportDB

Provides annotations for predicted transporters across sequenced genomes. TransportDB serves the membrane transporter annotation of 2777 complete genomes, comprising 2557 eubacteria, 164 archaea and 56 eukaryota. The database currently contains 860252 individual transporters, classified into 168 distinct families of transporters. In terms of each class of transporter, the database currently includes 457183 ATP-Dependent transport proteins, 32952 phosphotransferase system, 318233 secondary transporters, 29874 ion channels, 3273 outer membrane porins and 18731 unclassified transporter proteins. TransportDB also incorporates analysis tools that enable users to query the database on a number of levels.

MCPep

Explores the interactions of helical peptides of up to 50 residues with membranes of various types. MCPep is a server designed for non-experts wishing to perform Monte Carlo (MC) simulations of helical peptides in association with lipid membranes. The software simulates the peptide in the aqueous phase and membrane environments, both described implicitly. It reports the main determinants of peptide-membrane interactions, e.g. average location and orientation in the membrane, free energy of membrane association and the peptide's helical content.

TCDB / The Transporter Classification Database

Obsolete
A freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness.

ExTopoDB

Provides detailed, experimentally verified, annotation of the topology of α-helical transmembrane proteins. ExTopoDB is a database which is an up to date collection of experimentally verified topological information for α-helical transmembrane proteins. Compared to similar data sets, it contains the largest number of proteins with topology information derived from 1833 studies. Even for common entries, ExTopoDB holds a larger number of experiments for each entry, as most information was gathered from the literature. This web server also provides an analysis showing the increase in the prediction performance using topological data from ExTopoDB.

dbTEU / DataBase of Trace Element Utilization

Obsolete
Provides a biological trace elements database. dbTEU includes all known transporters and user proteins (excluding metal-binding chaperones and regulators) for five trace elements: Cu, Mo, Ni, Co and Se, in more than 700 sequenced organisms across the three domains of life. Approximately 16 500 proteins are stored in the database. In addition, this resource offers multiple search and browse options, such as BLAST homology searches. It also allows compilation of sets of trace element utilization proteins in individual organisms.

PlantsT

Combines experimental data regarding mineral composition of mutant and wild-type strains. PlantsT provides extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. It incorporates a unique user annotation and review feature aimed at acquiring expert annotation directly from the plant biology community. Graphical displays of insertion location, protein sequence motifs and domains, mineral fingerprints, trees and alignments are provided, as well as complete text and XML versions of the information.

ABCMdb / ABC Mutations database

Contains mentions of ATP Binding Cassette (ABC) protein mutations extracted from the literature using the MutMiner automated data mining method. The MutMiner pipeline was designed to recognize any mention of amino acid substitution occurring in text, including natural and experimental mutations found in genotypic or protein in vitro studies. Mutations were extracted from the full-text version of PubMed papers resulting from keyword searches for various ABC proteins.

TrSSP / Transporter Substrate Specificity Prediction Server

A web server that implements SVM models. Users can upload or paste protein sequences in Fasta format for transporter and substrate prediction. Six prediction modules have been provided on this web server: an amino acid composition based SVM, an AAIndex based SVM, a PSSM (SwissProt) based SVM, an AAIndex/PSSM (SwissProt) hybrid SVM, a PSSM (UniRef90) based SVM, and an AAIndex/PSSM (UniRef90) hybrid SVM. The TrSSP web server uses the amino acid composition module as the default.

MTDB / Medicago truncatula transporter database

A database of protein sequences of transporters of the model legume Medicago truncatula. Both automated search and manual curation were performed in identifying candidate protein sequences. Extensive annotations referring to each protein were generated, including basic protein function, genome locus, sequence annotations as well as transmembrane segment. A chromosome distribution map, text-based and BLAST search tools against known sequences of M.truncatula and known 3D structures of transporters were also created. A user-friendly web interface and regular updates make database valuable to researchers in related fields.

TransportTP

A genome-scale transporter prediction and characterization system called TransportTP that combined homology-based and machine learning methods in a two-phase classification approach. First, traditional homology methods were employed to predict novel transporters based on sequence similarity to known classified proteins in the Transporter Classification Database (TCDB). Second, machine learning methods were used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides.

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

Obsolete
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 activities of chemical compounds. hERGAPDbase aims to provide useful information for chemical and pharmacological scientists and enable easy access to electrophysiological experimental data on chemical compounds. The database provides links to MEDLINE entries for accessing abstracts of scientific papers related to the experimental data through click using the PMID.

TSdb / Transporter substrate database

Obsolete
A manually curated central repository that stores formatted information on the substrates of transporters. In total, 37608 transporters with 15075 substrates from 884 organisms were curated from UniProt functional annotation. A unique feature of TSdb is that all the substrates are mapped to identifiers from the KEGG Ligand compound database. Thus, TSdb links current metabolic pathway schema with compound transporter systems via the shared compounds in the pathways.