(ii) Clone identiﬁer, which queries the database using the Clone ID (iii) Vector, which queries selected properties of the vector such as cloning method (e.g. Gateway ), expression system (e.g. mammalian expression) and/or polypeptide features (e.g. ﬂuorescent tag) and (iv) Advanced search, a combined query using keywords, gene symbol/name, vector name, species, author name and/or publication information. The outputs yield a search results page listing the Clone ID, type of plasmid, links to the applicable model organism database, oﬃcial gene symbol, gene name, gene description, reference sequence, vector name and the vector’s selectable markers. Both Clone ID and vector name link to internal pages that provide detailed informa- tion including insert and vector sequence and a vector map. References to external annotations are also linked to their corresponding reference directly from the search output. Plasmids can be requested from the search results page by clicking the ‘Add to cart’ button. PSI-MR portal Database content. The PSI collection is a subset of the plasmid repository in DNASU. At DNASU, the ‘Plasmid of the Month’ features a PSI plasmid or plasmid collection that may be of particular use to researchers. For example, the Center for Eukaryotic Structural Biology (CESG) tobacco etch virus (TEV) protease expression construct (16) (Clone ID: TvCD00084286) enables the removal of fusion tags from recombinant proteins including those produced by many PSI plasmids and vectors that incorporate TEV protease sites. Once a month, we also highlight a PSI plasmid that encodes a protein of unknown function whose structure has been solved, which we hope facilitates in dissecting this protein’s biological function. Similar to the Functional Sleuth on the PSI SGKB (http://kb .psi-structuralgenomics.org/KB), this page highlights the protein structure, links to the plasmid in DNASU, and indicates other plasmids in our collection with similarity to the unknown protein. In addition to protein expression plasmids, DNASU distributes specialized vector backbones developed and optimized by the PSI Centers for protein expression in diﬀerent biological systems (e.g. mammalian, yeast, E. coli. etc.), for various experimental uses (e.g. overexpression in mammalian cells, protein puriﬁcation for crystallization or biochemistry, etc), and in speciﬁc applications (e.g. with a particular tag, selectable marker, promoter, induction properties, etc.) (24–28) (Table 2). DNASU distributes nearly 50 specialized vectors, including retroviral and lentiviral vectors used for cloning or expression in mammalian cells, specialized vectors for yeast and cell free systems, and vectors with various tags, markers and cloning strategies (17–21). These vectors provide a functional resource for biologists interested in applying this technology to their biological question of interest. Nucleic Acids Research, 2010, Vol. 38, Database issue D745 PSI-MR annotations. The PSI plasmid collection has the unique advantage that all of the plasmids were created as part of the well-organized and data-managed PSI program, which tracks a vast amount of experimental data for each plasmid. Thus, corresponding database structures have been included in DNASU to capture these features. All PSI plasmids have been tested for their ability to produce soluble protein, including detailed methods for puriﬁcation. This information has been documented by the PSI centers, and tracked in DNASU using a controlled vocabulary (e.g. protein_soluble, protein_not_soluble, protein_puriﬁed, etc.). This information allows researchers to quickly identify and sort for plasmids that will have the expression characteristics most suited for their experiment. Additional data compiled by PSI centers are assembled and incorporated into the PSI SGKB, and reciprocally linked to the PSI-MR plasmids. The PSI SGKB functions as a central portal where researchers can access all protein structures from the Protein Data Bank (PDB) (22), which includes over 4000 structures solved by the PSI eﬀorts, the PSI modeling portal, technology portal, publications portal and information from over 100 additional non- PSI biological resources. Also part of the PSI SGKB, the Target DataBase (TargetDB, http://targetdb.pdb .org) and Protein Expression Puriﬁcation and Crystallization DataBase (PepcDB, http://pepcdb.pdb .org) store detailed information about target selection strategy and progress, experimental protocols used, the experiments performed for a particular target or various iterations of the target (e.g. truncations or mutations), and the reasons for stopping work on a particular target (23,24). Cross-referencing between the plasmids and these resources helps engage the scientiﬁc community in this structural genomics eﬀort in addition to providing all available experimental information to assist researchers in identifying the functions of these proteins. PSI-speciﬁc search. The PSI-speciﬁc search options in DNASU leverage the additional information stored in the database for PSI plasmids. With the PSI-MR speciﬁc search, users can search for plasmids from a particular PSI Center, a speciﬁc target (searching by TargetDB ID) or with inserts that have been documented to (i) produce protein, (ii) produce soluble protein, (iii) produce puriﬁed protein and (iv) lead to a solved protein structure (searching by PDB ID). The PSI-speciﬁc search output then presents the information most relevant to the PSI and to researchers interested in these plasmids, without having to click through to the clone information page (Figure 1). This allows both PSI and outside researchers to reach experimental and structural information about each clone more quickly. Blast search. Many genes are assigned multiple names and often numerous ID numbers, leading to frustration by users who often know that a collection contains a gene of interest but are not sure which identiﬁer to use to ﬁnd it. Therefore, we have added a Basic Local Alignment Search Tool (BLAST) (25) search feature in order to search all of the cDNAs in our database to ﬁnd clones