Figure 6

Web user interface of PDIdb. (A) The database search engine. There are two search modes: basic and advanced. A basic search can be carried out by entering a PDB code or a keyword. The advanced search allows the user to make more complex queries through a dynamic expanding search form, by combining many subqueries that search all fields available in the database. (B) The result of the query is a table where each row shows basic information about the interface. When the user clicks on it, the row expands and a new table with detailed information, 2D and 3D molecular graphics is displayed. (C) For each interface, this information includes the protein and DNA features, as well as the detailed composition of the atomic contacts. (D) The user can inspect graphical information at both the sequence and structure level. A Jmol applet is available to explore the structure and the atomic interactions conforming the interface in three-dimensional space. (E) Sequences highlighting the contacting residues are available in FASTA format for further analysis (e.g. BLAST). (F) The protein-DNA complex can be also explored by means of NUCPLOT graphs, which map onto a plane direct or water-mediated hydrogen bonds between aminoacids and nucleotides.