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 dataset of Independent Structural Domains (ISDs) that are most likely to fold in isolation. IS-Dom was constructed by filtering domains from SCOP, CATH, and DomainParser using quantitative structural measures, which were calculated by estimating inter-domain hydrophobic clusters and hydrogen bonds from the full length protein's atomic coordinates. The ISD detection protocol is fully automated, and all of the computed interactions are stored in the server which enables rapid update of IS-Dom.
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.
Allows to find protein segments based on amino acid sequence and “Psi” and “varphi” dihedral angles. PHI-DAC is a database with entry composed of four pipe delimited fields: first and second fields contain the Protein Data Bank (PDB) identification (ID) and the amino acid sequence, and the third and fourth fields contain the “Psi”’ and “varphi” dihedral angles encoded in double characters. The online search engine can be helpful to the scientific community by easing the identification of conformation homologs and distilling information from the PDB.
Provides a compilation of protein mutant data, providing information on functional and/or structural influences brought about by amino acid mutations at specific positions of a protein. PMD is an online resource is unique in two respects: (i) almost all proteins are included, except for natural mutants of the globin and immunoglobulin families; (ii) natural as well as artificial mutants are covered, including random and site-directed mutants.
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