Results 31 to 40 of about 773,776 (302)
KINtaro – protein kinase-like database
BMC Research Notes, 2023 Abstract Objective The superfamily of protein kinases features a common Protein Kinase-like (PKL) three-dimensional fold. Proteins with PKL structure can also possess enzymatic activities other than protein phosphorylation, such as AMPylation or glutamylation. PKL proteins play a vital role in the world of living organisms, contributing to the
Bartosz Baranowski +2 more
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Context-specific interactions in literature-curated protein interaction databases
BMC Genomics, 2018 Background Databases of literature-curated protein-protein interactions (PPIs) are often used to interpret high-throughput interactome mapping studies and estimate error rates.
R. Greg Stacey +3 more
doaj +1 more source
How Far Are We from the Completion of the Human Protein Interactome Reconstruction?
Biomolecules, 2022 After more than fifteen years from the first high-throughput experiments for human protein–protein interaction (PPI) detection, we are still wondering how close the completion of the genome-scale human PPI network reconstruction is, what needs to be ...
Georgios N. Dimitrakopoulos +2 more
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Pfam: the protein families database [PDF]
Nucleic Acids Research, 2013 (Uploaded by Plazi for the Bat Literature Project) Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described.
Finn RD +12 more
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Characterization of Protein Complexes and Subcomplexes in Protein-Protein Interaction Databases
Biochemistry Research International, 2015 The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions.
Nazar Zaki +2 more
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Evaluating deterministic motif significance measures in protein databases
Algorithms for Molecular Biology, 2007 Background Assessing the outcome of motif mining algorithms is an essential task, as the number of reported motifs can be very large. Significance measures play a central role in automatically ranking those motifs, and therefore alleviating the analysis ...
Azevedo Paulo J, Ferreira Pedro
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Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework [PDF]
, 2015 The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes.
Arighi, Cecilia +7 more
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The Protein-DNA Interface database [PDF]
BMC Bioinformatics, 2010 The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype ...
Norambuena Arenas, Tomás. +1 more
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Improving classification in protein structure databases using text mining
BMC Bioinformatics, 2009 Background The classification of protein domains in the CATH resource is primarily based on structural comparisons, sequence similarity and manual analysis.
Jones David T +2 more
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Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome
mSystems, 2023 Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa.
Elliot M. Lee +8 more
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