D790 Nucleic Acids Research, 2011, Vol. 39, Database issue DATABASE ORGANIZATION AND ACCESS REPAIRtoire is a relational database that links together the aforementioned data sets, which can be queried via ﬁve menus, ‘DNA DAMAGE’, ‘PATHWAYS’, ‘PROTEINS’, ‘DISEASES’ and ‘PUBLICATIONS’ (Figure 1). DAMAGE: We collected information about 85 differ- ent types of damage in the DNA (as of October 14, 2010). Many of them describe general classes of damage events such as single-strand breaks or base loss that are inde- pendent of the local sequence). About 60 chemical com- pounds that cause DNA damage were connected to the according types of damage. Of all lesions, 36 could be connected to a single molecular structure (e.g. point mutations and nucleotide modiﬁcations such as 1-hydroxypropyl-adenine). Each type of damage is described on its own sub-page, which includes information about the potential source (e.g. spontaneous formation, intermediate in some DNA repair process, etc.), proteins that may recognize its presence in the DNA, keywords that facilitate analyzing its context, and literature links. For 36 types of damage with unique chemical structures, REPAIRtoire displays the structure in 1D (using a SMILE code), 2D and 3D (with the JMol JAVA applet), and provides atomic coordinates for download in the .mol format. PATHWAYS: This menu provides access to data about eight pathways (DDS, DDR, BER, NER, MMR, HHR, NHEJ, TLS) from three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. These pathways are represented as graphs visualized with PyGraphviz (http://networkx.lanl.gov/pygraphviz/), in which the nodes represent DNA states, and the edges represent the reactions between them, e.g. enzymatic reac- tions. All edges of the (sub)graph, i.e. arrows that connect the images, are hyperlinked to static ‘reaction’ windows comprising one or more panels that display basic informa- tion about the selected reaction. All nodes of the graph, e.g. DNA–protein complexes at various stages of the repair process, are hyperlinked to static windows comprising detailed information about the given stage of DNA repair. All protein components of each state/ complex are also hyperlinked to individual protein pages. PROTEINS: As of October 14, 2010, REPAIRtoire stores information about 69, 78 and 154 proteins from E. coli, S. cerevisiae and H. sapiens, respectively, and their Figure 1. Contents of REPAIRtoire database.