What is ProAffiMuSeq?

ProAffiMuSeq is a webserver to calculate the binding free energy change (ΔΔG in kcal/mol) upon mutation in protein-protein complexes. It uses functional information, sequence-based features and conservation scores in a regression model to predict ΔΔG in kcal/mol.

What is the advantage of using ProAffiMuSeq?

ProAffiMuSeq uses functional information, sequence-based features and conservation scores to predict the change in binding affinity (ΔΔG value, kcal/mol) upon mutation in protein-protein complexes. It does not require structural data as input. Thus, it can be used for protein complexes for which no structure is available.

Why is my input is not being accepted by the server?

There are a number of reasons why our server may not accept a given input. Please ensure that:

• The sequences are in FASTA format
• The chain identifier is specified in the header, like so: "> chain A"
• There are no unusual characters, numbers or other symbols in the input.
• The mutations are in the specified format: wt-chain-position-mutation
• One mutation per line
• No extra empty lines or spaces

What is the best method to assign functional class?

In practice, protein sequences are annotated with a specific function based on homology. You can get the UniProt ID of your proteins and determine the function (such as enzyme, inhibitor, antibody, G-protein, receptor etc.) using the information given in UniProt. Also, there are a few methods available for predicting protein function from sequence (if the UniProt ID is not available). Please refer to the Critical Assessment of Functional Annotation (CAFA) paper for available methods and their performance. Once you have assigned the functions for all the protein sequences in the complex, you can see which of the given functional classes the complex is most likely to belong to.

What programs can I use to find the secondary structure for the antibody mutations?

Online resources for predicting secondary structure include:

I would like to test mutations in many protein-protein complexes /
I would like to do a systematic Ala scanning for all the residues in a protein-protein complex.

We intend to provide a systematic Ala scanning option in a future version. Meanwhile, please contact us if you need to run large jobs.

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