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HRaP / HomoRepeats and Patterns
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.
PHI-DAC / Protein Homology database through Dihedral Angle Conservation
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.
PiQSi / Protein Quaternary Structure Investigation
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.
Provides access to the result of repeat protein domains, obtained from the amplification of population-genetic signal by constructing a motif-based multiple sequence alignment (motif-MSA). Intensification is a resource for annotating variants in 12 protein-protein interactions (PPI) repeat protein domains (RPDs). The database contains data files for ankyrins (ANK), annexins (ANX), armadillos (ARM), cadherin repeats (CA), fibronectin type 2 domains (FN2), fibronectin type 3 domains (FN3), leucine-rich repeats (LRR_TYP), spectrin repeats (SPEC), tetratricopeptide repeats (TPR), ubiquitin-interacting motifs (UIM), WD40 repeats (WD40), and WW domains (WW).
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.
Provides data about protein-ligand binding sites. SitesBase contains pre-calculated all-against-all binding site similarities which can be used for rapid retrieval and examination of other binding sites with similar structure. It provides three ways to search for a query site: (1) a PDB code, (2) a ligand three-letter code, corresponding to the Residue name in PDB format, (3) a keyword or phrase. The database can be used to corroborate functional similarity given sequence or fold similarity.
Helps scientists explore the functional role of C-termini in proteins of interest. C-Terminome contains thousands of C-terminal minimotifs with known function. Functions of other C-termini can be investigated based upon predictions inferred from experiments in rodents, predicted from known consensus sequences for minimotifs functions, and from new anchored consensus sequences on the C-terminus. The C-terminome web system enables a new approach for connecting proteins with poorly understood functions to other proteins that have more established roles in molecular reactions, pathways, or cell processes.
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