نتایج جستجو برای: pfam database
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Approximately, 10% of the world population is facing challenge food allergy in direct or indirect way. In this study, a genome-wide identification and annotation novel putative allergen from almond performed. Initially, whole proteome (31,000 proteins) was scanned by Allergenonline, publically available database already reported allergens different sources. The detailed analysis suggests that t...
With this poster [11], we present the SYSTERS protein family database, an attempt to classify all available protein sequences. In particular, we focus on the capability of the web interface to assist in in-depth analyses of special protein families. We demonstrate this by an analysis of a specific family of transmembraneous metal ion transport proteins characterised by the so called cation effl...
The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein do...
Automatic identification and annotation of protein domains is a major challenge for genome sequencing projects. Simple transfer of the annotation from the overall most similar protein with a known function is relatively reliable for prokaryotic proteins, but often produces misleading and incomplete results for multi-domain proteins, which are common in higher organisms. An alternative approach ...
In this report, various bioinformatics tools were employed to find sequence and structure homologs of a protein given its sequence. These tools include BLAST, PSI-BLAST, PFAM, ClustalW, T-Coffee, SAM-T99, SAM-T02, SingalP, TMHMM, and RasMol. Further information about genetic and metabolic functions of this protein was gathered from multiple online databases, including Saccharomyces Genome Datab...
The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. Analysis has been carried out for different levels of protein similarity, yielding a hierarchical organisation of clusters. The database pr...
DOMINE is a database of known and predicted protein domain interactions compiled from a variety of sources. The database contains domain-domain interactions observed in PDB entries, and those that were predicted by eight different computational approaches. DOMINE contains a total of 20 513 unique domain-domain interactions among 4036 Pfam domains, out of which 4349 are inferred from PDB entries...
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, liter...
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This...
BACKGROUND Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. How...
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