TOPDOM: Conservatively Located Domains and Motifs in Proteins

Related databases

HTP

The Human Transmembrane Proteome database and web service are comprehensive resources of the α-helical human transmembrane proteins. It contains topology and structure information about the human α-helical transmembrane proteins classified into reliability levels. First level is proteins with known 3D structures, second level is proteins with experimentally established topology, third level is proteins with conservatively appearing domains or motifs on one side of the membrane, fourth is proteins proved to be exists, and the last level contains proteins predicted from the annotated human genome database.

PDBTM

PDBTM is the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB). The database was created by scanning all PDB entries with TMDET algorithm. You can read more about PDBTM in our articles and in PDBTM manual.

TOPDB

The Topology Data Bank of Transmembrane Proteins (TOPDB) is currently the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information. The database collects the details of various experiments carried out to learn about the topology of particular transmembrane proteins. The experimental techniques include fusion with reporter enzymes, glycolysation studies, protease accessibility, immunolocalisation, etc. In addition to literature-derived data, an extensive collection of structural data was also compiled from Protein Data Bank (PDB) and from Protein Data Bank of Transmembrane Proteins (PDBTM) by utilising the TMDET algorithm.

UniProt

UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

Localodom

LocaloDom (Localo-orientations of Domains) is a database that provides information about TM topologies and TM helix numbers of around 3,000 eukaryotic Pfam domains. The TM topology information was constructed primarily from 1) descriptions of proteins in SWISS-PROT, 2) combined with the prediction results of Phobius algorithms. These domains are used to predict accurately the TM topologies of both soluble and TM proteins with TM proteins with the additional function of correcting falsely predicted TM helices.

Pfam

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

Prosite

PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. PROSITE is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids.

Prints

PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.

Smart

The Simple Modular Architecture Research Tool (SMART) is an online resource used for protein domain identification and the analysis of protein domain architectures.

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