Exercises for STRING and STITCH, given as part of the EMBO Practical Course 'Computational aspects of protein structure determination and analysis: from data to structure to function' at the EBI in Hinxton (Sept. 10, 2010)

1. http://string-db.org/ http://stitch-db.org/ Tutorial: STRING and STITCH<br />Michael Kuhn, Biotec, TU Dresdenmichael.kuhn@biotec.tu-dresden.de<br />These two databases are tools for exploring the interactions of proteins and chemicals. STRING concentrates on protein–protein interactions and integrates genomic evidence with data from experiments, manually curated databases and the literature. STITCH additionally collects information on associations between chemicals and proteins.<br />You can do several things with STRING and STITCH. If you quickly want to get information about a protein or chemical, you can enter them and look at the interaction partners. It’s also possible to submit multiple items; for example when you find that several proteins cause the same phenotype in a screen, you can check if they have common interaction partners. Lastly, you can also download the whole database of interactions and use it in computational screens.<br />Both databases work with snapshots of genomes and source databases, so you will not find very recently published data. Nonetheless, you will get a good idea on what is known for particular molecules.<br />Discovering protein–protein interactions<br />Imagine that you have just solved the structure of the Archaeoglobus fulgidus protein AF2331, and you have found that is has an unusual fold. Now, you would like to find potential interaction partners for a follow-up studies. Go to the STRING homepage http://string-db.org/ and search for AF2331. Select the Archaeoglobus protein. Look at the network and at the table of interaction partners below. What are the associations based upon? (Compare the colors of the edges to the table header, or click on edges to find out.)<br />Click on the “Neighborhood” button below the table. It will show you that the proteins are part of the same operon. Going back to the network, click the “more” button. An additional interacting protein appears. You can click on the green edge in the network to get more information on the source of the association.<br />Go back to the network again and, after clicking on AF_0211, select “add this node to input nodes.” This will expand the network, and some characterized proteins appear. Now, you see other types of edges. Click on the edge connecting fen and pcn and explore the sources of the interaction. (Note that few proteins have been studied in Archaeoglobus and therefore most of the information comes from similar proteins from other species.)<br />Context for chemicals<br />Suppose you would like to design inhibitors for the enzyme enoyl reductase from Toxoplasma gondii. How could you quickly get an overview of the existing data on this enzyme? Go to the STITCH homepage: http://stitch-db.org/ . Enter the protein name “enoyl reductase.” If you begin to enter the organism name “Toxoplasma,” you will notice that it is not yet in the database of genomes. However, you can search for related organisms by using the clade “apicomplexa” as organism name. Click “go” and see which species is found. <br />You will see a network of interactions with proteins (spheres) and chemicals (capsule-shaped). Among the chemicals, you will notice both metabolites and drugs, although the database does not distinguish between them. Click on the different items to see what they are. In interactive mode you can also drag the items around to better see the edges. <br />Change to the actions view. Now, the edge colors symbolize different types of interactions, as you can see from the table header. Look at the edge between triclosan and FabI: How do they interact? How do you explain the apparently contradicting information? <br />Let’s try to find as much information as possible by increasing the number of shown interaction partners. You can does this with the “interactors shown” menu in the box at the bottom of the page. Select “no more than 50 interactors” and then “update parameters.” Now, you will on one side see a cluster of metabolites, and on the other side various drugs. We can get rid of most metabolites by disabling the “database” and “text-mining” checkboxes at the bottom of the page. (Why?) If you change to confidence view, you will notice both strong and weak edges between PDB ligands and FabI. What is the difference? <br />When you inspect edges details, you can click on the “show” button to find more details. If there’s only one PDB structure, you will directly see information about it, otherwise you can click “info” for any of them. Notice the link to the PDB on the top right. <br />Your protein or chemical of interest<br />If there’s still time left, look for your protein or small molecule of interest and see if you find something you didn’t know before. <br />