Help Page
This page provides help to the users of PPTStab on how to efficiently use the various modules. For each module implemented in PPTStab, we provide figures and descriptions on how to use them.
Prediction Module
This module predicts the melting temperature (Tm) of proteins using two different methods.
Type 1: Using Protbert Protein Language Model Embeddings
Step 1: Calculate the embeddings for your protein sequences using Protbert model; we provide our standalone to calculate the embeddings.
Step 2: Select the embedddings method and appropriate flag for your sequences based on their condition i.e. Cell or Lysate.
Step 3: Input the embeddings file in the below file section or paste them in the text box and click the submit button.
Step 4: The result screen will show the predicted temperature values and the type of protein, please press on save as CSV button to save it to your device.
Type 2: Using Shanon Entropy (SER) Based Amino Acid Composition
Step 1: Input the protein sequences file in the below file section or paste them in the text box.
Step 2: Please select the SER method and appropriate flag for your sequences based on their condition i.e. Cell or Lysate.
Step 3: Select your desired physicochemical properties to be displayed along with Tm and click the submit button.
Step 4: The result screen will show the predicted temperature values and the type of protein, please click on save as CSV button to save it to your device.
Design Module
This module designs and evaluates single-residue mutants of a protein to identify and rank the most thermostable variants.
Step 1: Input the protein sequences file in the below file section or paste them in the text box.
Step 2: Please select the SER method and appropriate flag for your sequences based on their condition i.e. Cell or Lysate
Step 3: Select your desired physicochemical properties to be displayed along with Tm and click the submit button.
Step 4: The result screen will show the predicted temperature values and the type of protein along with other properties, please click on save as CSV button to save it on your device.