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

LACE: List-based Atomic Contact Excluder

Provide input for LACE to zero ASA of residues/atoms on a user-defined list):

Interpretation of residue/atom list:
Positive listing (zero ASA for listed items)
Negative listing (zero ASA for unlisted items)
User-defined residue/atom list (LACE format; see notes below):

Peptidic-structure ASA data (naccess-style format [e.g., generated using naccess via INCA]):

Notes:

  1. LACE facilitates designation of antibody-inaccessible residues and/or atoms thereof on user-defined lists (e.g., based on literature and/or direct inspection of models).
  2. LACE assigns a serial number to each polypeptide according to order of appearance in the input data, which may differ from the alphabetical order of PDB chain ID (A, B, C, etc.) assignments.
  3. To list one or more entire residues, use a series of semicolon-separated entries. Each entry must begin with a "word" of the form "X:" where X is the serial number of the polypeptide chain (1 for a monomeric protein or the 1st chain, 2 for the 2nd chain, etc.). The remainder of each entry must be a comma-separated series of individual residue numbers or ranges thereof. For example, the entry "2: 3, 5, 7-9" denotes residues 3, 5 and 7 through 9 of the 2nd polypeptide chain.
  4. To denote individual atoms rather than whole residues, the above format is extended by including a parentheses-enclosed list of PDB-style atom names after the respective residue number, with individual atom names on the list separated by the plus sign ("+"). For example, the entry "2: 3(N+CA), 5(C+O)" denotes the backbone nitrogen and alpha-carbon atoms of residue 3 as well as the backbone carbonyl carbon and oxygen atoms of residue 5 of the 2nd polypeptide chain.
  5. Combinations of residue- and atom-level notation are acceptable (e.g., "2: 3, 5(C+O), 7-9").