Experimental domain combinations

[nignatiadis]

We need to start adding experimental interactions and then check if the designer indeed takes these into account. Starting from tomorrow, could some of you (non-ilia) work on this?

Here's a suggestion, but feel free to add other papers to this issue and when you have worked on something, please mark it as done.

Doekel, Sascha, et al. "Non-ribosomal peptide synthetase module fusions to produce derivatives of daptomycin in Streptomyces roseosporus." Microbiology 154.9 (2008): 2872-2880.

Coding sequences used in this paper and which have to be added to the database:

• dptD
• lptD
• cdaPS3

Experimental fusions in this paper which have to be added to the database:

• T of dptD2 with C of cdaPS3-2
• others

Tested designer on above functionalities

• T of dptD2 with C of cdaPS3-2 (I'm afraid that in order to check this, also dptBC will have to be added to the database or we could do something hacky like temporary remove substrate specificity for 3-m-glu of cdaPS3-1)

@ilia-kats: Can you add any other papers that would be important to have in this list and would possibly be easier for us to check if the designer implementation works?