Results 31 to 40 of about 8,374,602 (379)
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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Protein-protein interaction databases: keeping up with growing interactomes
Human Genomics, 2009 Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction
Lehne Benjamin, Schlitt Thomas
doaj +1 more source
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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An analysis of the Sargasso Sea resource and the consequences for database composition [PDF]
, 2006 Background: The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information. Unlike the protein sequences held in the current searchable databases, the Sargasso Sea sequences originate from a single marine ...
Cozzetto, D +3 more
core +4 more sources
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis [PDF]
, 2020 We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments.
Held, Jason M +3 more
core +2 more sources
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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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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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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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
doaj +1 more source
Uniclust databases of clustered and deeply annotated protein sequences and alignments
Nucleic Acids Res., 2016 We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30 and three databases of multiple sequence alignments (MSAs), Uniboost10, Uniboost20 and Uniboost30, as a resource for protein sequence analysis, function prediction ...
M. Mirdita +5 more
semanticscholar +1 more source