Deposition, proteomic data

The x,y,z coordinates of all atoms in published, refined three-dimensional structures have been deposited in the Protein Data Bank (Table 3-4).568 571 Many other related databases are available,572 e.g., covering molecular modeling,573 gene sequences, proteome data,574 and much, much more. A good way to keep up to date is to read the "computer comer" in Trends in Biochemical Sciences (TIBS). Most databases can be reached on the World Wide Web.572 A selected list is... 

The first step in constructing a cell signaling network model is to generate an in silica interaction network. Signaling components of interest are identified, and data on binary interactions are extracted from the experimental literature. Often times, the creation of an entire interaction map for a large network is beyond the scope of one laboratory therefore, public databases have been created in which newly discovered proteins and/or protein interactions are deposited (57-63). However, often data are included from studies that cover a broad range of protein interactions, such as proteomic studies or yeast two-hybrid screens, and frequently contain many potential false positives or negatives. Thus, it becomes necessary to critically examine each reference to verify the interaction data reported, as this in silica network is the basis of further study. 

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