Proteopedia: A collaborative, virtual 3D web‐resource for protein and biomolecule structure and function

Received for publication, June 29, 2010Eran Hodis‡, Jaime Prilusky§, and Joel L. Sussman¶*From the ‡Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science§Department of Biological Services, The Weizmann Institute of Science, ¶The Israel Structural ProteomicsCenter, Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100 IsraelProtein structures are hard to represent on paper. Theyare large, complex, and three-dimensional (3D)—four-dimensional if conformational changes count! Unlikemost of their substrates, which can easily be drawn outin full chemical formula, drawing every atom in a proteinwould usually be a mess. Simpliﬁcations like showingonly the surface of the protein or showing only a tracebetween its alpha carbons are preferred methods for rep-resenting the overall structure of a protein, and zoomed-in views showing all of the atoms in a certain part of theprotein can highlight important residues. Unfortunately,even these simpliﬁcations can look confusing when ﬂat-tened into two-dimensional images as in printed text-books and scientiﬁc publications. Some aspects of therelationship between 3D protein structure and proteinfunction are more easily conveyed to students using 3Drepresentations of proteins, such as physical models orcomputer-generated molecular visualizations.Proteopedia (http:/www.proteopedia.org) is a new col-laborative web resource with pages describing protein,nucleic acid, and other biomolecule structures—includingcomplexes—in interactive, virtual 3D [1]. A typical pagein Proteopedia, which strives for encyclopedia-stylepages, shows a rotating 3D protein structure (using Jmol,[2]) adjacent to descriptive text containing hyperlinkscalled ‘‘scene links’’ that can be clicked to elicit a changein the 3D structure to illustrate a point made in the text.Proteopedia is a wiki, like Wikipedia, so every member ofthe scientiﬁc community with a user account can createand edit pages in the website, and its scene-authoringtools make it simple to add ‘‘scene links’’ to any page.To properly attribute both credit and responsibility topage-authors, the bottom of every page lists the usersthat have edited that page; each listed user name linksto a biographical account page describing the user’seducational and professional background to help thereader determine page reliability. There are more than200 user-added pages and more than 65,000 automati-cally generated ‘‘seeded’’ pages representing every entryin the Protein Data Bank (PDB), updated weekly.Educators have found Proteopedia to be a usefulteaching tool, and several instructors have adoptedProteopedia into their classrooms. The most obvious useis viewing existing user-added pages on molecules of in-terest (e.g. mechanosensitive channels [3] and HIV-1 pro-tease [4]). However, even if a speciﬁc protein lacks auser-added page in Proteopedia, if its structure has beensolved then the structure at least has an automaticallygenerated ‘‘seeded’’ page for its PDB entry with a rotata-ble 3D structure and useful information including theabstract from the publication describing the structure,automatically generated ‘‘scene links’’ for ligands in thestructure, and coloring by evolutionary conservation [5](e.g. luciferase, 2d1s [6]). Instructors have also createdpages as tutorials to either project in class or assign forstudents to read (e.g. tutorials on structural templates [7],serine proteases [8], and Ramachandran plots [9]). OnProteopedia, these instructor-created tutorials can beshared with other educators, who can adapt them foruse in their own classrooms, all while protecting the orig-inal tutorial from unwanted changes. Finally, several edu-cators have assigned class projects involving the crea-tion of Proteopedia pages on particular molecules ofinterest. The students learn through teaching, and theyend up contributing to a scientiﬁc and educationalresource (see undergraduate student-authored photosys-tem II page [10] and graduate student-authored triose-phosphate isomerase page [11]). BAMBED readers are invited to visit the Proteopediawebsite (http://www.proteopedia.org) and request a freeuser account.Beginning with this issue of BAMBED, selected Pro-teopedia pages that review a speciﬁc topic, protein, ormolecule and pass peer review will be published in a newsubsection of the feature Multimedia in Biochemistry andMolecular Biology Education. The Proteopedia page fea-tured in this issue of BAMBED also represents one of thewinning pages in the Proteopedia ‘‘Page of the Year Com-petition’’ for 2009 [12]. Thirty-one pages were entered intothe competition, which invited Proteopedia page-authors