The mission of UniProt is to provide the scientific community with a comprehensive, high quality and freely accessible resource of protein sequence and functional information. The site provides UniProtKB (protein knowledgebase) consisting of Swiss-Prot and TrEMBL sections; UniRef that speeds up sequence similarities search; and UniParc a squence archive.
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ExPASy is the Swiss Institute of Bioinformatics (SIB)Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions.
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expression and localization of proteins in human tissues
Category: Protein informations
The human protein atlas shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images (Marx V., Nature 509:645, 2014).
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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
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The ProteomeTools project is a joint effort of the Technical University of Munich (TUM), JPT Peptide Technologies, SAP SE and Thermo Fisher Scientific. It is dedicated to translating the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. Over the course of the project, ~1.4 million synthetic peptides covering essentially all human gene products including important post translational modifications will be synthesized and analyzed u
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BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
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The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
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MAPU is the Max-Planck Unified Proteome DB. Mass spectrometry (MS)-based proteomics on body fluids, cell lines, red blood cells, liver. MAPU datasets can serve as reference proteomes in biomarker discovery.
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The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
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EMBL European Bioinformatic Istitute
Category: Gene information search, Protein informations
EBI (EMBL European Bioinformatic Istitute) home page provides a central access point to search several databases for information on genes, proteins, enzymes etc.
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PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
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PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs). In addition to providing an extensive, manually curated phosphorylation site database, other commonly studied PTMs are included in PSP.
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The Comprehensive Enzyme Information System
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The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), PDBe (Europe) and PDBj (Japan) whic act as data deposition, processing and distribution centers for PDB data (RP Josten et al, Nucleic Acid Res 39, D411, 2011).
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A protein knowledge-base. It includes entries on more than 20,000 proteins and nearly 200,000 posttranslational modifications.
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PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences.
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There are 214,684,311 structures available on the AlphaFold DB website, including 48 complete proteomes available for bulk download.
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Proteome Commons is a public proteomics database for annotations and other information linked to the Tranche data repository and to other resources. The site is a project management tool that functions like some social networking websites. Users register, sign into the system, create a new project, and then invite colleagues and collaborators to the project. Invitees are given permissions and responsibilities by the project’s creator.
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ChEMBL, an open-access database, contains more than 5 million interactions between proteins and ligands that have been published in peer-reviewed journals or reported by laboratories and screening centers . Under ChEMBL’s “Ligand Search” tab, you can enter a compound’s SMILES notation in the “List Search” box and click “Fetch Compounds.” On the next page, clicking on the ChEMBL compound identifier under the 2-D drawing takes you to the Compound Report Card page, which includes th
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The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource for selected/multiple reaction monitoring (SRM/MRM)-based proteomic workflows (See Kusebauch, U. et al., Cell 166: 766, 2016; Doerr A, Nature Meth 13:712, 2016)
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