Features
ISPRED-SEQ is a method for predicting the occurrence of Interaction Sites on a protein starting from its sequence.
The input sequence is firstly embedded using ProtTrans T5 and ESM-1v in order to produce a vectorial representation of 2304 features for each residue.
This entirely substitutes the need for traditionally hand-crafted features such as physico-chemical properties of the residues or sequence profiles derived from multiple sequence alignments.
Input
The required input is a protein sequence in FASTA format, of a length in the range of 50 to 5,000 residues.
The user may insert the FASTA in two different ways:
- copying and pasting the sequence in fasta format in the panel;
- uploading a FASTA file.;
Output
There are three sections in the result page:
- Visualize Results:
this section contains general info about the job, like the ID, the date of submission, the protein ID, the protein lenght and the number of Predicted Interaction Sites. - Sequence features view:
A graphical representation of predicted Interaction Sites (IS) and Non Interaction Sites (N), highlighted in yellow and blue, respectively, along with the computed probability. - Tabular results:
On the top-right of the table, there is a download button to download the results in a Tab-delimited text format.
Below, there is table with the results for each residue, detailing the prediction and the probability, with the possibility to filter by prediction or residue type.