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

INCA: Interface for Naccess Calculation of ASA

Provide input for naccess via INCA to calculate ASA:

Decryption key for naccess:
Peptidic-structure data (in PDB-style format [e.g., PDB data or PACT output]):

Sample INCA Input and Output:

No. Input Output PDB chain/s Remarks
1 epospdbv.pdb epospdbv.asa 1BUY A H atoms removed from NMR structure using spdbv
2 renspdbv.pdb renspdbv.asa 2I4Q A missing non-H atoms reconstructed using spdbv
3 ifnpacto.pdb ifnpacto.asa 1FG9 A-B disordered residues represented using PACT
4 urepdbxr.pdb urepdbxr.asa 1E9Z A-B PDB (X-ray crystallographic) data used directly
5 toxpacto.pdb toxpacto.asa 1PRT A-F disordered residues represented using PACT
6 ps1pacto.pdb ps1pacto.asa (none used) oligopeptides represented as disordered using PACT
7 ps2pacto.pdb ps2pacto.asa (none used) oligopeptides represented as disordered using PACT
8 ps3pacto.pdb ps3pacto.asa (none used) oligopeptides represented as disordered using PACT

Notes:

  1. Naccess is external to SAPPHIRE/SUITE. To obtain decryption key and use naccess, refer to naccess home page.
  2. Peptidic-structure data (PDB-style format) should be from suitable source (e.g., output of PACT, or an equivalent PDB file).
  3. Peptidic-structure data should contain explicitly specified ATOM record lines for all (i.e., ordered and/or disordered) constituent residues.
  4. Every ordered residue should be represented by a complete set of ATOM record lines for all its constituent non-H atoms (e.g., as reconstructed using spdbv).
  5. INCA filters out H-atom data prior to naccess ASA calculation and replaces the naccess-generated ASA value for each disordered-residue atom with 1.00 Å.