SUITE = PACT + INCA + SPIRE + RACE + LACE + SUIT

SPIRE: Spherical Probe Inaccessibility Residue Excluder

Provide input for SPIRE to zero ASA of residues inaccessible to a large probe sphere using molmol:

SPIRE residue-exclusion mode:
Neighbor-independent (considers ASA of each residue independently)
Neighbor-dependent (considers ASA of each residue and its nearest neighbor/s)
Radius of spherical probe (Å):
Peptidic-structure ASA data (naccess-style format [e.g., generated using naccess via INCA]):

Notes:

  1. Molmol is external to SAPPHIRE/SUITE.
  2. SPIRE zeroes ASA of residues within concavities accessible to solvent but inaccessible to antibody.
  3. SPIRE uses CalcSurface command of molmol, with precision of 2 (e.g., "CalcSurface 10 2" for [default] probe radius of 10 Å).
  4. 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).
  5. 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.