OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer. Archaeal, bacterial (gram±), chloroplast, ER, endosome, eukaryotic PM, Golgi, lysosome, mitochondrial (inner/outer), nuclear (inner/outer), peroxisome, secreted proteins, thylakoid, vacuole, vesicle, viral.
Database of protein subcellular localizations for bacteria and archaea, determined through laboratory experimentation and computational predictions.
The LocDB contains protein subcellular localization data of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana). Users can search for lists of proteins present in different cellular organelles, and can be used to populate the environment of a molecular landscape and set context for the protein(s) of interest.
The Organelle Database contains protein localization data to more than 50 organelles, subcellular structures, and protein complexes from model organisms including yeast and humans. Users can search for lists of proteins present in different cellular organelles and protein complexes, and can be used to populate the environment of a molecular landscape and set context for the protein(s) of interest.
The LOCATE database contains data describing the membrane organization and subcellular localization of human and mouse proteins. This database can be used to query the known location of proteins of interest within a cell. It also provides lists of proteins found in different cellular compartments. The list of proteins are not comprehensive, so other proteins relevant to the environment may be missing. This resource can then be used to populate the environment of a molecular landscape and set context for the protein of interest.
The Uniprot database can be used to find protein sequence and functional information. The information in this database can be combined with 3D structural data to determine the function of the whole protein as well as different domains of the protein. This information can be used to determine, for example, the regions of a membrane protein that are present inside or outside a cell, or the region of a protein that binds to DNA.
The Gene Ontology (GO) is a resource that compiles functional information on genes from the experimental evidence reported in peer-reviewed scientific papers. Once a list of genes or proteins of interest is collected for a molecular visualization, the genes and proteins can be queried in GO to learn more about their known functions.
The Human Protein Atlas is a histology and immunofluorescence tissue based human proteomics database, containing both normal and cancerous human tissue samples. This database contains stained histological tissue samples that show a protein of interest’s location on both the tissue and cellular level. It can be used to determine the most relevant cellular environment for a protein of interest.