Searching the Knowledgebase
The PSI-Nature SGKB can be searched by one-letter code protein sequence, plain text and Protein Data Bank identifier code. The following section describes how to use these search options.
Searching by Amino Acid Sequence or PDB id
The PSI-Nature SGKB maintains a database of the sequences of PSI protein targets and the sequences of all solved protein structures released by the Protein Data Bank. Sequence searches are performed using the BLASTP program with an E-value cutoff of 10. To search for a particular protein sequence, enter the one-letter amino acid sequence in the search form, select the by Sequence radio button and press Search. An example query is available by selecting the by Sequence radio button, pressing "example query", and then pressing the Search button. These options are highlighted in the following figure.
The PSI-Nature SGKB maintains a database of the identifier codes for all experimental structure entries released by the Protein Data Bank. To search for a particular Protein Data Bank entry, enter the structure's 4-letter ID code in the search form, select the by PDB id radio button and press Search. An example query is available here (2I9Y) to explore these features as well. These options are highlighted in the following figure.
Results of a Sequence or PDB ID Search
The results of sequence and PDB ID code searches are first displayed as a summary of available records relating to the input query. An example of a Results Summary is shown in the following figure.
To view query result details individually, select the DB REPORT tab at the top of the summary page. From this summary, you can view the type of information you seek (structures, annotation, models, targets, protocols, or materials) by clicking on the appropriate tab, as shown below.
The Structure(s) section provides the essentials details about any structures matching the input query. If the query results for a sequence search are displayed, then the percent of sequence identity (percent exact sequence similarity) with the input sequence is displayed for each matching structure entry (I), as well as the E value (E). The Structure(s) section presents: a link to the RCSB PDB Structure Explorer Page, a link to a collection of molecular images from the RCSB (when available), and a download option for the PDB format structure data file. Other essential information about the PDB structure entry is also provided such as: PubMed and DOI for the primary citation (when available), title, authorship, deposition and release dates, and experimental method. If the structure was solved by a PSI project then this information is provided along with the associated PSI Target identifier. In the example report below, 3 structures match the input query.
The Annotation(s) section presents a collection of links containing structural and functional annotations for the matching structure entry. In the figure of a typical annotation section below, links are provided to the databases PDBSUM, Proteopedia, Pfam, InterPro and Gene3D.
Computational Model(s) associated with a query sequence or structure are shown in this section. In the case of a sequence query, the number of models that have been predicted for this sequence are presented along with a link to the details for each model. In the case of the PDB ID query, the number of computational models which are based on information from this experimental structure is presented. All of these results are obtained by a remote query to the PSI Protein Models Portal, which collects and maintains this information. In the example below, there are 5 models from three modeling databases available.
Information about matching structural genomics targets is shown in the Target(s) section. A link to the Target Registration database, TargetDB, is provided for each matching target along with the current progress for the target (e.g cloned, expressed, purified, in PDB). Additional information about each matching target may also be provided such as source organism, sequence database identifiers and sequence family membership. A typical example target result section is shown below.
The Protocol(s) section provides links to the Protein Expression Purification and Crystallization Database (PepcDB). The first link identifies the matching target, and the second link provides an alignment of this result with the query sequence, along with the % Identity value (I). Additional links for protocols descriptions associated with each protein production step are also provided.
The last tab provides information about the availability of relevant target DNA clone materials at the PSI Materials Repository (PSI MR). The PSI MR is a resource that provides an on-line searchable database of archived PSI genetic materials, transfer, storage and maintenance of PSI plasmids in a highly quality-controlled manner at centralized on-site and off-site locations, and the facilities to distribute PSI plasmids and supporting information for research purposes within the U.S. and abroad. In this example, two target clones are available for purchase. Selecting these clones will transfer you to the PSI-MR PlasmID website.
Plain Text Search
The PSI-Nature SGKB maintains a 'plain text' index of all content in webpages and documents at the PSI Center websites. To the search the PSI-Nature SGKB by plain text, enter the appropriate words in the search form, select the by Text radio button and press Search. These options are highlighted in the following figure. An example query (ATP Kinase) is available by selecting the "by plain text" radio button, selecting the example query link, and pressing the Search button.
The results of the text search are presented as list of pages containing the input search term (e.g. ATP kinase) as shown in the following figure.
Clicking on the Structural Publication tab will show all structural PSI-published articles that contain the query term; in this case, all structural publications that contain the term ATP Kinase. By selecting the "Read More" link, the full citation of the artlcle will be provided, including abstract and PubMed identifier.
Clicking on the Methodological Publication tab will show all PSI-published articles containing the search term that focus on methodology. By selecting the "Read More" link, the full citation will be shown. In this way, you too can propel your own research using innovative methods derived by the PSI's high-throughput pipeline.
If you have any further questions regarding the use of this website, please contact us at comments@psi-structuralgenomics.org.