Because setting up the several library components necessary for running SCOPmap is both time-consuming and computationally expensive, we will list results here. These are the results of SCOPmap run on the structures added in the weekly updates of the PDB. SCOP v1.65 was used as the library for Feb 21, 2005 and previous weeks. SCOP v1.67 was used as the library for Feb 28, 2005 - July 24, 2005. SCOP v1.69 was used as the library for Jul 25, 2005 and after. ---------------------------------------------------------------------------------------------------------- The two formats of these results are as follows: 1. output.domainlist Each assigned (or unassigned) region is listed in this file. Each domain is listed on a separate line, which includes the PDB id name and chain identifier, the protein name from the PDB file, the range of this domain, the SCOP superfamily ID to which it is assigned (or "X" if no assignment is made), the confidence of the assignment (see below), and a short description of the SCOPmap results for this domain. Unassigned regions less than 20 residues within a longer chain are ignored (i.e. not listed in this file). - The confidence range is 0 to 4, with 4 being most confident. 1 through 4 refer to superfamily level assignments. If a fold level assignment is made, it is given confidence 0. 2. output.assigned.fa This is fasta-style output including only the domain assigned at the SCOP superfamily level. In each entry, the definition line includes the pdb ID and chain ID, the range of the domain, the SCOP superfamily ID to which it is assigned, and the confidence value of the assignment. The sequence is taken from the CA chain of the PDB file. ---------------------------------------------------------------------------------------------------------- These queries were first clustered at 95% identity (over 95% of the length of the chain). If your PDB-of-interest is not included in these outputs, check if some other repesentative was used in its place: see "representative_chains" file, the first entry on each line is the query for which SCOPmap was actually run. We hope to update these lists on a regular basis.