A database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2737 CATH superfamilies. The current Gene3D (v14) release has expanded its domain assignments to approximately 20 000 cellular genomes and over 43 million unique protein sequences. Amongst other updates, we have improved our Functional Family annotation method. We have also improved the quality and coverage of our 3D homology modelling pipeline of predicted CATH domains. Additionally, the structural models have been expanded to include an extra model organism (Drosophila melanogaster).
Comprises over 300 000 domain structures and over 53 million protein domains classified into 2737 homologous superfamilies. Cath-Gene3D contains over 300 000 structural domains. It groups protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH-Gene3D is a member of ELIXIR - the European-wide project providing high quality and sustainable infrastructure for biological information.
A structural classification of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses.
A database of pairwise, structure-based alignments for structurally analogous motifs in proteins. Applications of this database may range from protein evolution studies, e.g. development of remote homology inference tools and discriminators between homologs and analogs, to protein-folding research, since in the absence of evolutionary reasons, similarity between proteins is caused by structural and folding constraints.
Offers different information on protein structural domains. 3Dee is an online database that hosts alternative domain definitions for a given protein and manages domains into structural hierarchies and sequence. This database includes: structures alignments for families of domains, and non-redundant set of structures and sequences. Furthermore, this repository enables users to regenerate previous version of the database.
Allows users to visually inspect the classification and, by adjusting geometric parameters, to probe the variation in helical packing across the protein data bank (PDB). ACC is focused on the automatic identification and classification of a subset of previously unclassified coiled-coil structures, namely the α-helical barrels. It integrates classification scheme showing regions of protein-structure space that are currently unoccupied.
Includes all protein segments of a length up to 15 residues contained in the Protein Data Bank (PDB). Searching the database for loop candidates takes less than 1 s on a desktop PC, and ranking them takes a few minutes.
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