Frequently Asked Questions



What are the main advantages of FuncLib?

What type of proteins can be submitted to FuncLib?
FuncLib calculations work best on soluble, single domain proteins. We are currently developing FuncLib versions for membrane proteins and binding interfaces.
It is highly recommended to work on a PROSS stabilized variant of your protein.

Can FuncLib be used without a structure?
FuncLib 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 sequnce to avoid bias the PSSM (see here for details).

Can I submit an NMR structure?
FuncLib 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 FuncLib calculation take?
FuncLib 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 interpret the different variants names?
One of the results files is the sequence space. This file contains a list of allowed amino acids at each diversified position (the WT identity is placed first). For example:
   106A    ICHLM
   132A    FL
   271A    LIR
   217A    ML
In the other output files, the name of each mutant relates to the sequence space; and each mutation is represented with 2 digits. For the sequence space shown above,a mutant with the name 04010202 has the following sequence: I106L, 132 is not mutated (numbered 01), L271I and M217L. The mutant that contains in its name only .01. symbols (0101010101) is the WT.

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 FuncLib. 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 rosalie.lipsh@weizmann.ac.il
Good Luck!