Proteins are essential to life, and the shape of a protein is critical for its function. The Protein Data Bank (PDB) contains a wealth of structural information, but few biologists take full advantage of it. Thus, we developed Aquaria (http://aquaria.ws), a publicly available web resource that streamlines and simplifies the process of gleaning insight from protein structures. Aquaria also extends the reach of known structures by matching them with protein sequences of unknown structure.
Shown here is the Aquaria page for human tumor suppressor protein p53. (i) Initially, the PDB structure estimated to be most relevant is shown. Dark and very dark residues indicate conserved and nonconserved substitutions, respectively, between the structure and the wild-type p53 sequence (ii). Aquaria also shows all related PDB structures, grouped by region of match (iii). Clicking on a group loads the top-ranked structure; clicking on a group number shows a tree view of structures organized by oligomeric state (iv). InterPro and UniProt features (v) can also be mapped onto structures.
