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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
Integrated web visualizations for protein-protein interaction databases [PDF]
, 2015 BACKGROUND: Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions.
Holzinger, Andreas +2 more
core +3 more sources
SwissPalm: Protein Palmitoylation database [PDF]
F1000Research, 2015 Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from
Mathieu Blanc +6 more
openaire +2 more sources
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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Do protein–protein interaction databases identify moonlighting proteins? [PDF]
, 2011 One of the most striking results of the human (and mammalian) genomes is the low number of protein-coding genes. To-date, the main molecular mechanism to increase the number of different protein isoforms and functions is alternative splicing. However,
Amitai +31 more
core +2 more sources
The impact of sequence database choice on metaproteomic results in gut microbiota studies [PDF]
, 2016 Background: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences.
Addis, Maria Filippa +10 more
core +4 more sources
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
openaire +7 more sources
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