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User's Manual

The flow diagram of using our server

Now we upload the sample test file to show how to use our server.

1. Login

For registered user, you can sign in with your username and password. For testers, click on the "Instant entry" button. If you forget your password, you can reset your password with your mailbox by clicking on 'Forgot Password?'.

We use a system of user management in order to give every user a separate space to handle their uploaded drugs. Users can register freely and easily by clicking on the "Register" button. If you do not want to register, just click the "Instant entry" button, You'll automatically login as the 'guest' user.

2. Upload a drug molecule

After logging in, you will see a page which allows you to upload a drug molecular.

Click on the "Browse" button to upload a drug file. We support multiple file formats including mol, mol2, pdb, pdbqt and sdf (How to generate and prepare a mol2 file?). Usually, our server could check the suitability of your molecule. If the file suitability does not meet our demand, the results would be incredible. In order to protect the accessibility of other users, your uploaded file should not exceed the limitation of 20 kb. You can download our sample file naphthylamine.mol2 and upload it for a quick test.

3. Wait the interactome of your drug molecule to be constructed (several hours)

When your drug molecule file is uploaded correctly, our program starts to put your molecule in a queue automatically. Our server implements Autodock Vina3 to generate the docking scores of your molecule towards our library targets. You can click on the "Refresh" link to see the progress. If you upload our example file, it takes only several minutes to complete, however, for others it might take much longer.

If you are a registered user, you will see a list of your submissions like below. Click on the "Detail" button, you will first see detailed information of this drug.

If you login as the guest user (by clicking on the QuickLogin botton), you will be inform a special link to your access submission. Please bookmark this link for later access. If you input your email address before submission, the notification email would also include this special link.

4. Check the drugs predicted to interact with your molecule and their indication information

After the docking progress is finished, you can see the predicted interactions of your drug molecule towards our library drugs. The "N/A" symbol in some fields does not hamper the result. You will not see the interactome of your molecule across the targetable proteins or the association of Interaction Profile unless the progress rate reaches 100%.

In the middle of this page, you can see a list of library drugs with drug-drug predictions to interact with your uploaded molecule as well as the probability of an estimated prediction (interaction confidence) based on their interaction profiles of the Chemical-Protein Interactome. The known indications for the library drugs are provided, suggesting the underlying risk of your molecule interacting with drugs for specific treatments. You can enter a keyword in the "Search" box and press enter, to search for a drug name or indication. You can click on the "Clear" button to cancel your searching operation. The predictions were made by our optimistic model from our data mining result of drug-drug interactions based on chemical-protein interactomes. Some drugs have more than one isomers or ionization states. We keep all of them and name them as "somedrug 1", "somedrug 2" ... as more options for the users to analyze. You can view the difference of their structures via Jmol Applet. You can also download the whole table by simply clicking on the "download" link, and you can drag the downloaded text file into Excel to see the whole table.

By clicking on the button "See Chemical-Protein Interactome" at the top, you can view candidate off-targets that tend to interact with your molecule. In the right column of this page, you can view the basic information and 3D model of your molecular.

5. Check the detail binding patterns of the interacted drug as well as your molecule

Click on the "Detail" button to see the detail binding patterns of the interacted drug as well as your molecule. At the right side of this page you will see the drug name, DrugBank ID, description, indication and its 3D model for the library drug. In the center of this page, it displays a table of the interaction profile of both the specific library drug as well as your molecule, where the binding scores, or docking scores between the two drugs and a list of active binding targets are shown.

According to our optimistic model of the data mining results, the drug molecule tends to interact with the protein if docking score is less or equal than -8.4. Now we only display the red shared targets with strong bindings for both drugs in this page.

Currently, we have 611 putative targets in our library, which is continuing to be added. In this "CPI visualization table", only the targets that have relatively strong bindings (docking scores less or equal than -8.4) towards both drugs will be shown. The "Class" column indicates whether this target is pharmacokinetic (PK) or pharmacodynamic (PD). You can also click on the download link to download a full table. By the way, you can click on any score to visualize the 3D image of the specific binding pattern.

6. Check the candidate off-targets tend to interact with your molecule

In step 4, Click on the "See Chemical-Protein Interactome" button to see candidate off-targets that tend to interact with your molecule. The server suggests candidate off-targets that tend to interact with your molecule. You can click on the "Visualization" button to visualize the binding pattern, with amino acid residues around 6.4Å of the drug molecule colored in the Applet.

The Docking Score fields represent the interaction strength of the molecule to the protein.

We are now using JSMol as a HLML5 molecular visualizer without requiring Java platform. It is capable on new versions of Firefox, Chrome and Internet Explorer 9+. For Internet Explorer 8 users, the visualizer will be Java-based JMol. If you cannot see the Jmol Applet, or receive a message like "You do not have Java applets enabled in your web browser", you need to install Java Runtime Environment (JRE). JRE could be downloaded at for free. You can choose "label on/off" to show/hide the labels of the amino acid residues around 6.4Å of the drug molecule.

7. Log out

If you want to logout or switch to another account, you can click "Log out" in the left navigation menu, or close your browser, the session will automatically end.


1 L. Yang et al, SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome. Nucleic Acids Research (Web Server issue). 2009;37:W406-12.

2 H. Luo et al, DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome. Nucleic Acids Research (Web Server issue). 2011;1(7).

3 O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry. 2010;31:455-46.

4 H. Luo et al, DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome. Nucleic Acids Research (Web Server issue). (2014): gku433.