Results 11 to 20 of about 497,683 (263)
Current successes and remaining challenges in protein function prediction
Frontiers in Bioinformatics, 2023 In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes.
Constance J. Jeffery
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Databases in Protein Crystallography [PDF]
Acta Crystallographica Section D Biological Crystallography, 1998 Applications of structural databases in the protein crystallographic structure determination process are reviewed, using mostly examples from work carried out by the authors. Four application areas are discussed: model building, model refinement, model validation and model analysis.
G J, Kleywegt, T A, Jones
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Gene and protein nomenclature in public databases
BMC Bioinformatics, 2006 Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of ...
Zimmer Ralf, Fundel Katrin
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The Pfam Protein Families Database [PDF]
Nucleic Acids Research, 2000 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.
Bateman, Alex +12 more
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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
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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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