mining to locate biomolecular interaction information in the scientific literature. The name or accession number of a protein can be entered and PreBIND will scan the literature and return a list of potentially interacting proteins. BIND BLAST is also available to find interactions with proteins that are similar to the one specified in the query. BIND offers several “features” that many other proteomics databases do not include. The authors of this program have created an extension to traditional IUPAC nomenclature to help describe post-translational modifications that occur to amino acids. These modifications include: acetylation, formylation, methylation, palmitoylation, etc. the extension of the traditional IUPAC codes allows these amino acids to be represented in sequence form as well. BIND also utilizes a unique visualization tool known as OntoGlyphs. The OntoGlyphs were developed based on Gene Ontology (GO) and provide a link back to the original GO information. A number of GO terms have been grouped into categories, each one representing a specific function, binding specificity, or localization in the cell. There are 83 OntoGlyph characters in total. There are 34 functional OntoGlyphs which contain information about the role of the molecule (e.g. cell physiology, ion transport, signaling). There are 25 binding OntoGlyphs which describe what the molecule binds (e.g. ligands, DNA, ions). The other 24 OntoGlyphs provide information about the location of the molecule within a cell (e.g. nucleus, cytoskeleton). The OntoGlyphs can be selected and manipulated to include or exclude certain characteristics from search results. The visual nature of the OntoGlyphs also facilitates pattern recognition when looking at search results. ProteoGlyphs are graphical representations of the structural and binding properties of proteins at the level of conserved domains. The protein is diagrammed as a straight horizontal line and glyphs are inserted to represent conserved domains. Each glyph is displayed to represent the relative position and length of its alignment in the protein sequence. Accessing the database The database user interface is web-based and can be queried using text or accession numbers/identifiers. Since its integration with the other components of BOND, sequences have been added to interactions, molecular complexes and pathways in the results. Records include information on: BIND ID, description of the interaction/complex/pathway, publications, update records, organism, OntoGlyphs, ProteoGlyphs, and links to other databases where additional information can be found. BIND records include various viewing formats (e.g. HTML, ASN.1, XML, FASTA), various formats for exporting results (e.g. ASN.1, XML, GI