Open Access Highly Accessed Software

The PubChem chemical structure sketcher

Wolf D Ihlenfeldt1, Evan E Bolton2 and Stephen H Bryant2*

Author Affiliations

1 Xemistry GmbH, Hainholzweg 11, D-61462 Königstein, Germany

2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA

For all author emails, please log on.

Journal of Cheminformatics 2009, 1:20  doi:10.1186/1758-2946-1-20

Published: 17 December 2009

Abstract

PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

Graphical abstract