[1][2][3][4] The site contains a page for all of the entries in the Protein Data Bank (PDB), as well as pages that are more descriptive of protein structures in general such as acetylcholinesterase,[5] hemoglobin,[6] and the photosystem II[7] with a Jmol view that highlights functional sites and ligands.

It employs a scene-authoring tool so that users do not have to learn JSmol script language to create customized molecular scenes.

A web browser is all that is needed to access the site and the 3D information; no viewers are required to be installed.

Proteopedia was the winner of the 2010 award for the best website by The Scientist magazine.

Proteopedia is hosted at the Israel Structural Proteomics Center[9] at the Weizmann Institute of Science.