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 is structure 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.

I am facing issues with the display of the website on my browser.

The website may be best viewed using the latest version of a browser such as Google Chrome or Mozilla Firefox.

What is the jumbotron cover image about?

The cover image shows the beta-chain of the hemoglobin structure, one being the wild-type with Glutamic acid at position 6 (PDB code 1LJW), and the other bearing the Glu6Val mutation (which causes sickle-cell anemia; PDB code 1NEJ). The RMSD between the wild-type and mutated structure is 1.1 A. Glu6Val mutation causes deoxygenated haemoglobin to adhere and form twisted rod-like structures, which in turn cause red blood cells to assume a sickle shape. The cover image highlights the ability of a mutation to cause disease by altering interactions between proteins, even when structure may not undergo large conformational changes.