The NetSurfP-2.0 server predicts the following structural features; surface accesibility, secondary structure, disorder, and phi and psi angles. A single model, using a combination of Convolutional and Bi-Directional Long-Short Term Memory Neural Networks, predicts all structural features together.
The server requires protein sequence(s) in fasta format, and can not handle nucleic acid sequences.
Paste protein sequence(s) in fasta format into field marked by arrow A or upload a fasta file marked by arrow B . Click the submit button, marked by arrow C , when protein sequences are entered.
Depending on the sample size, MMseqs (batch) or HHblits (single) will automatically be selected to optimise computational time. Computational time can range from a couple of minutes to several hours depending on the queue and the sample size.
After the server successfully finishes the job, a Server Output page shows up. If an error happens during prediction a log will appear specifying the error.
Use the navigation bar ( arrow A ) to flip through the various output pages. The output can be exported in the format of CSV, JSON, NetSurfP-1.0 format and Zipped Archive by clicking "Export All" on the far right of the navigation bar ( arrow B ). The Zipped Archive contains the sequence profiles from HHblits/MMseqs and the NetSurfP-2.0 predictions. The default page is the Server Output, where a short description and summary of the prediction ( arrow C ), followed by a paginated list of the predicted protein sequences ( arrow D ). The search bar allows easy accessibility of viewing a specific entry. Each predicted protein can be also be exported separately using the Export button on the far right of the protein of interest.