ELM - The Eukaryotic Linear Motif
“ ELM is a computational biology resource for investigating candidate functional sites in eukaryotic proteins. Functional sites which fit to the description "linear motif" are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives.
The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive. ”
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PFam - Protein Families
“ The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function.
Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.
The data presented for each entry is based on the UniProt Reference Proteomes but information on individual UniProtKB sequences can still be found by entering the protein accession. Pfam full alignments are available from searching a variety of databases, either to provide different accessions (e.g. all UniProt and NCBI GI) or different levels of redundancy. ”
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UniprotKB
“ The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB and PIR are committed to the long-term preservation of the UniProt databases.
UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). Across the three institutes more than 100 people are involved through different tasks such as database curation, software development and support.
EMBL-EBI and SIB together used to produce Swiss-Prot and TrEMBL, while PIR produced the Protein Sequence Database (PIR-PSD). These two data sets coexisted with different protein sequence coverage and annotation priorities. TrEMBL (Translated EMBL Nucleotide Sequence Data Library) was originally created because sequence data was being generated at a pace that exceeded Swiss-Prot's ability to keep up. Meanwhile, PIR maintained the PIR-PSD and related databases, including iProClass, a database of protein sequences and curated families. In 2002 the three institutes decided to pool their resources and expertise and formed the UniProt consortium. ”
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PDB - Protein Data Bank
“ The Protein Data Bank (PDB) was established as the 1st open access digital data resource in all of biology and medicine (Historical Timeline). It is today a leading global resource for experimental data central to scientific discovery.
Through an internet information portal and downloadable data archive, the PDB provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). These are the molecules of life, found in all organisms on the planet.
Knowing the 3D structure of a biological macromolecule is essential for understanding its role in human and animal health and disease, its function in plants and food and energy production, and its importance to other topics related to global prosperity and sustainability. ”
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BioGRID
“ The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (thebiogrid.org). BioGRID currently holds over 1,740,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 70,000+ publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. ”
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PhosphoSitePlus®
“ PhosphoSitePlus® provides comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, acetylation, and more. The web use is free for everyone including commercial. ”
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