Algorithm 1 SIDEpro Pseudocode.

Calculate boxes: 3DboxBB, 3DboxSC, and 3DboxRot

Calculate neighbor sets: NbrBB, NbrSC and NbrRot

//set qij to be pij and remove clashing rotamers

for all residue i do

for all rotamers at residue j do

qij=pij

Evdw(i, j) = calculate equation (38)

if Evdw(i, j) > 1.0 then

remove rotamer j

end if

end for

end for

//calculate EBB

for all residue i do

for all rotamers j at residue i do

EBB(i, j) = calculate equation (39)

end for

end for

//calculate ESC

for all residue i do

for all rotamers j at residue i do

for all l, m ∈ NbrRot(i, j) do

ESC(i, j, l, m) = calculate equation (40)

end for

end for

end for

// update energies and probabilities until r converges

while any qij does not converge do

for all residue i do

//update energy of rotamers at residue i

for all rotamers j at residue i do

eij = calculate equation (41)

end for

//update probability of rotamers at residue i

for all rotamers j at residue i do

qij = calculate equation (42)

end for

end for

end while

for all residue i do

${\widehat{r}}_i=\underset{j}{\text{argmax}}{q}_{ij}$

end for

where

qij : updated probability of rotamer j at residue i pij : initial probability of rotamer j at residue i (from library) r : current set of rotamers i r̂i: predicted rotamer for residue i