Example of MEDUSA prediction for 1BINA

Let us consider the example amino acid sequence of leghemoglobin A extracted from PDB ID 1bin (chain A) (http://www.rcsb.org/structure/1BIN). The results of prediction for this sequence are available by clicking “Paste sequence example” link and submitting the job:


You can omit the first line with sequence name and also download file by using the "Browse" button.

It is recommended to fill your e-mail adress to receive a notification once the job has finished. To do so use the following form:


Once you push button your sequence is sent to the server for calculations. You are thus forwarded to the waiting page where you can observe your job progress. Eight stages are described in details at About page:


Finally, once job completed MEDUSA provides you with various predictions: 2-class prediction with strict threshold, 2-class prediction with non-strict threshold, 3-class prediction and 5-class prediction. You can download output with all the intermediate results as tar.gz archive:


You can also directly analyze the prediction results for your sequence using MEDUSA visualisation. The first plot reflects flexibility class attributed to each residue. The color indicates confidence of prediction in terms of the raw value returned by the network. Below the detailed classification results we also provide a part chart with the overall content of the predicted residues of each type in the protein composition. Here is the output example for the three classes classification of 1BINA protein:


Interpretation of the results

The main goal of MEDUSA is to provide information on the degree of flexibility of different regions for proteins without available three-dimensional structure. The attributed flexibility classes correspond to the ranges of normalized crystallography B-factor values (see "About" for the details). Such information is of clearly related to the protein secondary structure. Thus, fragments identified as rigid most probably make part of the structured part of the protein. Moreover, high ration of highly flexible fragments in protein structure an be on the contrary, an indicator of disorder.

Below you can see a three-dimensional structure of our example protein 1BINA colored according to the three-classes flexibility prediction following the pie-chart color scheme (from deep blue rigid fragments to orage describing flexibility):


In this example, the most rigid protein fragments were found in the middle of alpha-helices, while connecting loops are mostly identified as flexible. One can also notice that the degree of flexibility increases for the fragments exposed to the solvent. Finally, long loop on the top-left side of the protein is attributed to the intermediate flexibility class and has a more structured form than usual coil. The residues of this frament (80-85) are potentially forming a polyproline II structure according to PROSS, which can be an indicator of the potential interactions with other partner.