Table 2. JET² automated clustering algorithm.

	First round to detect main clusters
if #(T JET > 0.6)/N < 0.3 * f intfrac(N)—————–	• Test whether the evolutionary signal is too low: N, number of surface residues f intfrac(N), expected size of the interface #(T JET > 0.6)/N, proportion of highly conserved residues
then
choose SC3;
else
choose SC1;
end
detect cluster seeds;
if SC1 then
if Seeds = ∅————————————————	• Test whether SC1 found some seed: Seeds, set of seeds
then
choose SC3;
detect cluster seeds;
else
if $\frac{\sigma \left(s\right)}{\mu \left(s\right)}<\frac{1}{6}\frac{{\sigma }_{surf}}{{\mu }_{surf}}\text{,}$ for all s ∈ Seeds—————–	• Test whether the seed conservation signal is homogeneous: σ(s) and μ(s), dispersion and mean of the distribution of the scores computed over the residues in seed s σ surf and μ surf, dispersion and mean of the distribution of the scores computed over all surface residues
then
choose SC2;
detect cluster seeds;
end
end
end
add the extensions to the seeds;
add the outer layers to the clusters;
if SC1 or SC2 then	Second round to detect additional clusters using a complementary SC
choose SC3;
else
choose SC2;
end
detect cluster seeds;
add the extension to the seeds;
add the outer layers to the clusters;
combine clusters;	Merge main clusters with additional clusters <5Å away
scoreMax ← maxr ∈ C(score(r));	Extension of a cluster C
while $\mu \left(C\right)>scor{e}_{clus}^{CUT}$ do
newRes ← {};
for r ∈ {neighbors of C} do	score(r), score of the residue r μ(C), mean score computed over cluster C $scor{e}_{res}^{CUT}$, threshold score for residues $scor{e}_{clus}^{CUT}$, threshold score for clusters {neighbors of C}, ensemble of residues <5Å away from C
if $scor{e}_{res}^{CUT}<score\left(r\right)<scoreMax$ then
add r to newRes;
end
end
add newRes to C;
scoreMax ← maxr ∈ newRes(score(r));
end
newRes ← {};	Addition of an outer layer to a cluster C
for r ∈ {neighbors of C} do
if $\frac{\mu \left(C\right)\times \left|C\right|+score\left(r\right)}{\left|C\right|+1}\ge \mu \left(C\right)$ then	{neighbors of C}, ensemble of residues <5Å away from C
add r to newRes;
end
end
add newRes to C;