The PubChem chemical structure sketcher

The National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov webcite is widely known for its cluster of literature, biology, genomics, and chemistry databases which are freely accessible on the Web [1]. These databases register many tens of millions of hits per day from millions of users accessing the site via a broad range of Web browsers and operating system platforms. From experience gained in more than a decade of operation, NCBI has developed a set of principles concerning what kind of client-side technology can be deployed as a part of its Web services. These help to prevent access or support issues, specifically those pertaining to configuration or installation of the user's Internet access tools. Therefore, any technology which cannot be expected to work reliably with a standard client browser installation right out of the box, typically cannot be used in public NCBI Web services. For these reasons, NCBI Web pages traditionally allow only the use of basic HTML and JavaScript on the client, CGI/FCGI processes on the server, and nothing more.This approach has not been a severe limitation for the operation of the classic collection of databases served by NCBI. However, with the addition of the PubChem[2] suite of databases, an obvious problem arose. Chemical structure databases cannot be readily queried by structure in a reasonable fashion using purely textual input and standard HTML form elements. Users of chemical structure databases demand the capability to search by full-structure or substructure, with a graphical rendition of the query structure as input. Fragment name search, externally generated and pasted SMILES/SMARTS[3]strings, or upload of query files drawn with stand-alone chemical structure drawing programs are awkward procedures and do not yield a satisfactory user experience. It became very clear that the PubChem structure search system needed a method to allow users to draw their query structure interactively, in an integ