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 distinguish transmembrane from globular proteins. It also available to study any particular transmembrane protein and to find for example a binding site located in the lipid or in the aqueous phase.
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 proteins and peptides from approximately 350 organisms that represent approximately 3800 Protein Data Bank (PDB) entries. The database also indicates structural classification, topology and intracellular localization.
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 topology of all protein sequence in UniProt database by the CCTOP algorithm and scanning 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.
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 derived from the OPM database, PDBTM, or MPstruc. MP:PD is thus a sub dataset of the wwPDB and lists only proteins with at least one transmembrane helix.
Collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable. Motifs contained in MeMotif can be used in different biological applications, from the identification of biochemically important functional residues which are candidates for mutagenesis experiments to the improvement of tools for transmembrane protein modeling.
This database is a compilation of the predictions made by the Freeman-Wimley algorithm, which was shown to be among the most accurate predictor of TMBBs. Also included are N-terminal export signal peptide predictions made by the SignalP server.
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 offers a large-scale classification not restricted to proteins with known structure. The database includes eukaryotic and viral membrane proteins in the classification approach as well as higher-order hidden Markov models (HMM) and loop length patterns as an additional fold determinant.
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 crystallography, gene fusion, and other methods. This online resource includes only proteins of known 3D structure. It can be downloaded as a composite text file or searched using a java applet (MPtopo Querier) connected to an SQL based server.
Quantifies the structural distortion induced by a sequence motifs in alpha transmembrane segments. TMalphaDB contains 330 structures of α-helix bundles. To avoid redundancy, only one structure for each protein is selected according to resolution and resemblance to the native state. Each structure is characterized by the PDB identification code, protein name, Uniprot accession code, family name (according to OPM) and organism.
Membrane protein function and stability has been shown to be dependent on the lipid environment. CGDB is a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.
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 algorithm, which has been designed to process both representations of protein structure. Users has the possibility to upload protein models and their membrane assignments to database. Most of the protein structures in TMPL come from external databases and were selected for containing the term “transmembrane” in either their keywords, title or description.
Gathers transmembrane proteins and their helical membrane-spanning domains. TMBase is a resource that contains, besides the sequence itself, both annotational items extracted from SwissProt and additional data fields calculated from the sequence or taken from other sources. The database provides information such as the location of the Transmembrane (TM)-domain in the sequence, the sequence of the flanking region, the putative orientation of the transmembrane proteins and the TM-helices, or the types of membranes the proteins are associated to.
Integrates publicly available data of the shed membrane proteins. SheddomeDB is a database for the identification of experimentally validated shed membrane protein. It provides numbers of membrane proteins for reviewing the shedding information. The database included membrane-bound shed markers associated with numerous cellular processes and diseases. SheddomeDB can be a useful resource for discovering membrane-bound shed markers.
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