Ultra-fast and Large-Scale Protein Structural Neighbor Searching


Getting Started

Input data must be protein structure files in PDB format. The input structure should contain at least one chain identifiers forming the interface definition. Please follow the descriptions for the input format. Users could leave their email address; MADOKA will send the similarity searching and aligning results to the address. Please refer to Figure 1.

Figure 1. Job submission.

The server will check the validity of the input structure, and once confirmed, process to the secend step to select the query protein chain. If the selection is done, please click the button "submit" to run the job (Figure 2). Users will then be directed to the result page with job status. The analysis could also be retrieved by job ID in the result page.

Figure 2. Select the query protein.

MADOKA will provide a compressed file including all of similarity searching and aligning result files to download once the job finished. There will be MADOKA result and superposed traces of Ca atoms between query protein and PDB database protein. In order to visualize the 3D structures of the aligning resutls, users can click "view". (Figure 3)

Figure 3. Results.

The information of 3D structures aligning results is showed by Jsmol with a list of the most simialar proteins in the PDB database with the query protein, the list is sorted by TM-score. User can click "compare" to view the aligning traces. (Figure 4).

Figure 4. Results and visulization.

An example

Please follow the link to see an example.