MPA-Pred: Membrane Protein complex binding Affinity Predictor

FREQUENTLY ASKED QUESTIONS

  1. What is MPA-Pred?
    2. MPA-Pred is a webserver to calculate the binding affinity (ΔG in kcal/mol) of membrane protein-protein dimer complexes. It has been developed based on the different sequence- and structure-based features in a regression model to predict ΔG in kcal/mol. For more information about the features kindly refer to the publication.
  2. What is the advantage of using MPA-Pred?
    3. MPA-Pred uses both structure- and sequence-based features to predict the binding affinity (ΔG, kcal/mol) in membrane protein-protein complexes. The method classifies the complexes based on the type of pass: single-pass or multi-pass. Also, single-pass complexes are further classified based on their functions, showing improved performance.
    Note: This method requires structural data as input. If PDB is not available for the complex, kindly model the complex using AlphaFold or any other method and upload the pdb file.
  3. Why is my input is not being accepted by the server?
    4. There are a number of reasons why our server may not accept a given input. Please ensure that:
    • All * fields are inputed
    • The mentioned PDB ID and chain identifiers are correct and available in the PDB database
    • The user uploaded PDB file match with pdb format
  4. What are the units and notations used in MPAD for thermodynamic and kinetic parameters?
    5. Firstly, you can get the UniProt ID of your proteins and find the type of pass information given in the subcellular location in UniProt. In order to determine the functional class, you can use the function information given in UniProt. Once you have assigned the functions for both the proteins in the complex, you can see which of the given functional classes below, the complex is most likely to belong to.
    Functional Class Description
    Enzyme Complex having one or both the interacting partners that function as an enzyme
    Receptor Complex having one or both the interacting partners that function as a receptor
    Transporter Complex having one or both of the interacting partners as transporters
    Miscellaneous Complex which do not fall in any of the above classes
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