SPIRE zeroes ASA of residues within concavities accessible to solvent but
inaccessible to antibody.
SPIRE uses CalcSurface command of
molmol, with precision of 2 (e.g., "CalcSurface 10 2" for [default]
probe radius of 10 Å).
Neighbor-independent residue-exclusion mode considers ASA of each residue
individually, such that a residue is regarded as inaccessible if its total
ASA is found to be zero (using SPIRE probe sphere).
Neighbor-dependent residue-exclusion mode considers ASA of each residue and
its nearest-neighbor residue/s in sequence, such that a residue is regarded
as inaccessible only if its total ASA is zero and it is not flanked by any
residue whose CalcSurface-calculated total ASA is positive.