Explain how the algorithm selects suitable domains from the database

[Hetitus]

This could be visually accomplished in the frame where the module order is presented to the user for the first time (see image). Similar to the next input frame there could be a drop down for every domain. in each drop down there could be the scoring of the chosen domain but also the scoring of worse domains that could be also suitable. Then the user gets a feeling for the selection possibilities he has...

[ilia-kats]

This is not that easy, unfortunately. For example, for a D amino acid,
the algorithm considers both incorporating an L amino acid followed by
an epimerization domain and directly incorporating the D enantiomer, and
selects the version with the lowest total cost for the entire NRPS. The
selection of a T domain also depends on whether it is followed by an E
or a C domain, as there are two different types of T domains for these
cases.

The point is, the algorithm does not score each domain individually, but
rather the whole NRPS. Displaying the user an alternative for a specific
domain may be misleading, since actually using this domain in the
algorithm may have a higher cost than building the NRPS with a different
strategy.

[Hetitus]

Well, then lets do both. I would still prefer a 'drop down' containing the domains with a worse score for this particular NRPS - strategy. At the same time we could give some advise how the NRPS could be possibly improved by another assembly strategy. There could be some messages flashing up in the same window that point out these specific options that you mentioned above… Let's meet for further discussion…