Which strategy for mutate? Mutate All tool versus scripts/hand
|Opened by:||Bruno Kestemont|
|Opened on:||Saturday, November 22, 2014 - 11:29|
|Last modified:||Wednesday, November 26, 2014 - 11:49|
I read from the Wiki that the mutate tool does not try all possible mutation, but it uses a "Monte carlo" algorithm in order to save time (see http://www.pnas.org/content/97/19/10383.full).
1) Is it correct that when mutating only one segment, all possible AAs are tested and Monte Carlo does not apply?
2) What happens with the position of the side chains after mutating? Is a shake still necessary? or does the mutate function also look for the best sidechain position?
3) Does the mutate function only test the "preferred" AAs for a specific SS? For example, it would not try an AA that likes sheet in a helix. Or does it test anything just based on a statistical algorithm with pairs of any AAs?
And now the implications for the design strategy.
4) Just after the SS first hand design, does it make sense not to mutate all, but instead, mutating manually (or with recipes) to the best desired AAs (like hydrophobic, or helix preferred where we want an helix) instead of to let the mutate tool do the work?
Many questions. Thanks to anybody who can help.