TOPDB Topology Data Bank of Transmembrane Proteins
Topology, Structure and Prediction.
Database revision: (4190 entries, 75211 topology data) Quick search:    

Database status

Database revision:
Revision date: 01/01/70
Entries: 4190
Topology data: 75211
Alpha helical proteins: 4067
Beta barrel proteins: 123
PubMed links: 4270
PDB links: 12816
UniProt links: 4190
Visitors: 584207

Related servers and databases

Servers developed in the Institute of Enzymology

HMMTOP

The HMMTOP transmembrane topology prediction server predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins by utilizing an unsupervised hidden Markov model. In this method the user is allowed to submit additional information about segment localization to enhance the prediction power. This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments.

TMDET

TMDET algorithm determines the most possible localization of the membrane relative to the protein structure by using the protein 3D structure only, and gives the annotation of the membrane embedded part of the sequence. This web interface of the TMDET algorithm allow scientists to determine the membrane localization of structural data prior to deposition or to analyze model structures.

TOPDOM

TOPDOM is a collection of domains and sequence motifs located conservatively in one side of transmembrane proteins. The database was created by scanning well annotated transmembrane protein sequence in UniProt database by specific domain or motif detecting algorithms. The identified domain or motif was added to the database if it was uniformly annotated in the same side of the membrane of the various proteins in UniProt database. Transmembrane proteins subset of UniProt were scanned by using hmmpfam algoritm with Pfam and Smart domain databases, prosite scan with Prosite motif database and fingerprints algorithm with Prints database.

DAS-TMfilter

DAS-TMfilter is a modification of the dense alignment surface (DAS) transmembrane helix prediction method that achieves a substantial decrease in the false positive error rate in. The modified DAS method, the DAS-TMfilter algorithm, has an unchanged high sensitivity for TM segments (~95% detected in a learning set of 128 documented transmembrane proteins). At the same time, the selectivity measured over a non-redundant set of 526 soluble proteins with known 3D structure is ~99%, mainly because a large number of falsely predicted single membrane-pass proteins are eliminated by the DAS-TMfilter algorithm.

Psortb

PSORT-B includes new analytical modules designed to capitalize on new discoveries and observations in protein sorting, and benefits from a training dataset of over 1400 proteins of known localization. Its focus is on precision over recall to faciliate accurate predictions, at the expense of not making as many predictions as other methods may make.

Other servers

  • DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)
  • MemBrain - Transmembrane protein structure prediction (HongBin Lab)
  • Memsat - Membrane Helix Prediction (University College London)
  • Octopus - Prediction of membrane protein topology and signal peptides (Stockholm University)
  • Philius - Transmembrane Topology Prediction Server (Yeast Resource Center)
  • Phobius - A combined transmembrane topology and signal peptide predictor (University of Copenhagen)
  • PredictProtein - Prediction of transmembrane helix location and topology (Columbia University)
  • Pro and Prodiv - Alpha-helical transmembrane protein topology prediction methods utilizing hidden Markov models and evolutionary information (Stockholm University)
  • SignalP - Predicts the presence and location of signal peptide cleavage sites (Technical University of Denmark)
  • Scampi - Prediction of membrane protein topology from first principles (Stockholm University)
  • SOSUI - Prediction of transmembrane regions (Nagoya University, Japan)
  • TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)
  • TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH)
  • TopPred - Topology prediction of membrane proteins (France)

Databases, data sets

  • HTP - The Human Transmembrane Proteome Database
  • OPM - Orientations of Proteins in Membranes (OPM) database
  • PDBTM - PDBTM is the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB).
  • TMHMM training set
  • White lab - Database of membrane proteins of known 3D structure
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