Frequently Asked Questions

What are the main advantages of AffiLib?

What type of proteins can be submitted to AffiLib?
AffiLib calculations work best on interfaces of soluble proteins. We are currently developing AffiLib versions for membrane proteins.
We also offer FuncLib- a version of AffiLib for diversifying enzyme active-sites to improve or change catalytic functions. In case you know of expression problems due to misfolding, it is possible to work on a PROSS stabilized variant of your protein.

Can AffiLib be used without a structure?
AffiLib must receive an X-ray structure as input.
If your protein does not have a solved X-ray structure, you can use as input structure a homology model you trust. The sequence homology between the protein of interest and the input structure must be at least 40%.
A homologous structure can be found using hhpred And the model for your protein sequence can be generated with SWISS-MODEL

Can I submit a structure with missing density (missing residues/loops)?
Yes, you may submit a structure that has some missing residues. However, you will need to provide the sequence of the whole protein sequence to avoid bias the PSSM (see here for details).

Can I submit an NMR structure?
AffiLib does not support NMR structures. Though, if you tweak the NMR-based pdb file to look as if it is based on a crystal structure (having all atoms appearing only once), you may use this structure.
However, we strongly recommend avoiding NMR structures, as they are typically not accurate enough for these kind of calculations.

How long does a AffiLib calculation take?
AffiLib is comprised of 2 steps, and each may take a day or two. After the first step is done, you will be sent an email with a link to enter more parameters to control the calculation of the second part. When the second step is done, you will be sent an email with the results.

What do the result files include?
When results are ready you will get an email with a zip file attached. It will include a file named ReadMe.txt with a detailed explanation of the results. Please read the ReadMe.txt file carefully.
A shorter description of the results:

How to proceed towards experimental validation?

How to proceed when receiving an error email?
Errors are most likely due to user's wrong input.
In the error email you have a list of all the parameters that you submitted to AffiLib. Go over each parameter and make sure it is correct.
Below is a list of common user errors:

For any further questions and troubleshooting, please contact
Good Luck!