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From this alignment, we determined all the couples of positions that were statistically never found mutated together, that we called SL and focused on the SL set, which are accessible to the solvent, and not too far apart spatially.
By "a locked set" we mean "an SL set plus all the invariant positions".
By "SL set", we mean a set of SL couples that are connected to each other.
To compromise viral escape, it should dock on an invariant position or on an SL set.
Trait values calculated using linear regression of SL (set to 50 mm) and ecomorph.
We choose to add also the invariant position being in the vicinity of the SL set.
Similar(50)
From an amino acid sequence alignment of the HIV protease, we detected the potential SL couples, potential SL sets, and invariant positions.
Although unlike other teams, we did not discriminate the proteases from treated versus non-treated patients when collecting our initial lot of sequences, all these SL couples are included in our 290 SL couples and none of them are included in our SL sets.
Most SL sets are not maximal cliques, but some SL sets are quite close to being maximal cliques.
So we propose to add larger "SL sets" rather than one single SL couple.
We indeed add invariants to SL sets in order to extend our targets into "locked sets".
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com