Quick search

On the homepage, you will see a search box. Type in a protein name or ID (such as A4 or Q9UBN7) and press the Enter key or click on the magnifier button. You will be directed to a new page that shows the detailed information of the protein you searched for.

Advanced search (experimental)

On the homepage, click on the Advanced Search link above the search box, or in the navigation bar. You will go to the search child page where you can use more search options. The data loading may take some time, so please wait patiently. On the top right corner of the page, you will see a switch button that says Search Switch. The switch button is on by default, which means you can only search for one item at a time. If you want to search for multiple items at once, you can turn off the switch button by clicking on it. You will see three tabs on the page: Proteins, Diseases and Go Enrichment. Each tab shows a table of data related to that category. You can enter a protein name or ID in the Proteins tab to see its details and networks. You can also click on the items in the Diseases tab and the Go Enrichment tab to see their networks.

Detail page

The detail page shows the specific information of a protein, such as its name, ID, function and related publications. You can scroll down to see more information in the detail table. Below the detail table, there is another table that shows the interactions of the protein with other proteins. This table lists the names, IDs and scores of the interacting proteins. You can enter a protein name or ID in the search box above the interactions table to see its details on a new page. You can also view the PPI network visualization along with the detail table.

Network page

The network page shows a graphical representation of a protein and its interactions. The protein is shown as a node (a circle) and its interactions are shown as edges (lines) connecting to other nodes. The nodes and edges have different colors and sizes depending on their properties. You can zoom in and out of the network by using your mouse wheel or the buttons on the bottom right corner of the page. You can also drag and drop the nodes to rearrange them. On the network page, you can click on some of the nodes or edges to see more information about them on a pop-up window. The pop-up window will show you the protein docking visualization and scores of the selected node or edge. Protein docking is a process of predicting how two proteins fit together and interact with each other. The visualization shows you how they look like when they are docked and the scores tell you how well they are docked.

The cross disease module viewer

The cross disease module viewer can be accessed from the button "Cross disease protein modules" below the disease subnetwork buttons on the home page. Please click to visit the visualization of the cross disease modules of any of the two disease subnetworks (default AD with PD). You can use checkboxes to select the diseases of interest. Click submit to update the visualization.

Protein docking

On the network page, you can see more information about protein docking by clicking on some of the nodes or edges. You can also send your own protein pdbs and docking results to chenhj@zju.edu.cn or yekaizhou@zju.edu.cn for feedback. Protein pdbs are files that contain the three-dimensional coordinates of atoms in a protein molecule. Docking results are files that contain the predicted positions and orientations of two proteins when they are docked together. You can use some software tools (such as AutoDock or HADDOCK) to generate these files from your own protein data.

Data Download

The download page provides the data files of NDAtlas.