In proteins, a structural motif describes the connectivity between secondary structural elements, such as hairpin, loops, and helixes. Protein motif database gathers information on specific structure occurrences, motif-based molecular switches, structural domains, and more.
Provides projection of protein domains, functional sites and exon boundaries on protein and coding gene sequence. SitEx concerns proteins with known 3D structure and corresponding genes. It is useful for search for the structural similarity between the polypeptides that do not necessarily possess the sequence similarity. The database allows rational design of novel proteins composed of fragments encoding individual exons from distinct genes.
A database of occurrence of homorepeats and disordered patterns in different proteomes. HRaP is aimed at understanding the amino acid tandem repeat function in different proteomes. Therefore, the database includes 122 proteomes, 97 eukaryotic and 25 bacterial ones that can be divided into 9 kingdoms and 5 phyla of bacteria. The database includes 1,449,561 protein sequences and 771,786 sequences of proteins with GO annotations. Through this web server, the user can do the following: (i) search for proteins with the given homorepeat in 122 proteomes, including GO annotation for these proteins; (ii) search for proteins with the given disordered pattern from the library of disordered patterns constructed on the clustered Protein Data Bank in 122 proteomes, including GO annotations for these proteins; (iii) analyze lengths of homorepeats in different proteomes; (iv) investigate disordered regions in the chosen proteins in 122 proteomes; (v) study the coupling of different homorepeats in one protein; (vi) determine longest runs for each amino acid inside each proteome; and (vii) download the full list of proteins with the given length of a homorepeat.
A database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. The data sets are freely available for download.
Consists of a database that curates experimentally validated motif-based molecular switches and a prediction tool to identify possible switching mechanisms that might regulate a user-submitted motif of interest. switches.ELM helps to extend knowledge and direct research on how motifs mediate cooperative decision-making in a context-dependent manner and direct reliable and robust cell regulation.
Compiles information related to quaternary structure (QS) of proteins. PiQSi provides a repository of structures recorded in other databases and permits users to investigate for homologs of a protein sequence. Searches can be made by sequence or by PDB ID and the application displays information relative to each protein including the symmetry of its QS, its function and its sequence length, as well as links to the corresponding literature and databases. The data can also be curated by the users.
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