Provides access to experimentally derived information about the human proteome including protein–protein interactions (PPIs), post-translational modifications (PTMs) and tissue expression. HPRD is an integrated knowledgebase for genomic and proteomic investigators. The database also includes (i) PhosphoMotif Finder that contains known kinase/phosphatase substrate and binding motifs, (ii) links to a signaling pathway resource called NetPath, (iii) a distributed annotation system, called Human Proteinpedia for enhanced community participation and allows the use of BLAST for querying mRNA/protein data.
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).
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.
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.
Provides consensus structural annotations and 3D models for sequences from model organisms, including human. These data are generated by several UK based resources in the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, THREADER, PHYRE.
Comprises over 300 000 domain structures and over 53 million protein domains classified into 2737 homologous superfamilies. CATH employs a number of structure-comparison and sequence comparison tools to assist the manual curation of these remote evolutionary relationships. It provides superfamilies aligned with a number of related resources such as InterPro, Pfam, SCOP, UniProtKB.
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.