Parameter setting for the commonly used methods              FSSP              : SCOP-defined domains were extracted from original PDB files; DaliLite (version 1.5) was then used to produce pairwise structural alignments and their corresponding sequence alignments. PSIBLAST   : Each SCOP query was used with blastpgp to search a version of the non-redundant sequence protein database that contains masked low complexity regions (performed with seg program, window length size = 20) for 4 rounds of PSI-BLAST to create a position-specific scoring matrix or profile. This profile was then used to search a database of sequences from scop1.48 to produce SCOP-SCOP alignments. The blast command used for searching the masked nr database (named nrhc) with a SCOP query named d1abc was :         blastpgp -e 10 -h 0.0001 -N 18 -f 8 -F T -j 4 -d nrhc -i d1abc.fasta -C d1abc.check -o d1abc.nrhc The search of scop1.48 was performed with this blast command :         blastpgp -e 10 -N 16 -f 8 -F F -R d1abc.check -d scop148 -i d1abc.fasta -R d1abc.check -o d1abc.scop Blastpgp version 2.1.10 was used and the non-redundant database used was created on July 1, 2001. Periodically we will perform these calculations again with an updated nr database. BLAST         : The blast program bl2seq (version 2.1.3) was used to obtain pairwise alignments of all SCOP family and superfamily pairs. FASTA        : FASTA33 was used to search a database of all SCOP sequences in the same superfamily as the query to produce pairwise alignments with parameters -e 10 -z 15. The -z parameter is used to obtain an accurate estimate of statistical significance even though the target database does not contain unrelated sequences. CLW-Pair   : Clustal W (version 1.8) was used to align pairs of SCOP sequences with the BLOSUM62 matrix.
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