# Evaluation Ruleset for SCOP 1.75 Benchmarks

For more information see the more detailed page on the outdated ruleset for SCOP 1.61 here.

```sub Criteria{
#1.75 version
#Takes as an input two SCOP classifications, and returns a flag.
#1 if they're the same, 0 if it's ambiguous, and -1 if they're different
my \$flag=-1;
my \$one=\$_[1];
my \$two=\$_[2];
my \$cf1;
my \$cf2;
my \$sf1;
my \$sf2;
my \$fa1;
my \$fa2;
my %rossmann=('c.2',0,'c.3',0,'c.4',0,'c.5',0,'c.27',0,'c.28',0,'c.30',0,'c.31',0);
#these all have notes in SCOP

if (\$one =~ /^(\w\.\d+)(\.\d+)(\.\d+)/){
\$fa1="\$1\$2\$3";
\$sf1="\$1\$2";
\$cf1="\$1";
}
else{
print STDERR "Error parsing classification: \$one\n";
}
if (\$two =~ /^(\w\.\d+)(\.\d+)(\.\d+)/){
\$fa2="\$1\$2\$3";
\$sf2="\$1\$2";
\$cf2="\$1";
}
else{
print STDERR "Error parsing classification: \$two\n";
}

#Same fold ambiguous
if (\$cf1 eq \$cf2){
\$flag=0;
}
#plain right
if (\$sf1 eq \$sf2){
\$flag=1;
}

#Fixed as of SCOP 1.63!
##Unless Membrane all-alpha
#if ((\$sf1 eq 'f.2.1' or \$sf2 eq 'f.2.1') and \$fa1 ne \$fa2){
#\$flag=-1;
#}

#TIM barrels
#first 7 similar -note in SCOP-
if ((\$sf1 eq 'c.1.1' or \$sf1 eq 'c.1.2' or \$sf1 eq 'c.1.3' or \$sf1 eq 'c.1.4' or \$sf1 eq 'c.1.5' or \$sf1 eq 'c.1.6' or \$sf1 eq 'c.1.7') and (\$sf2 eq 'c.1.1' or \$sf2 eq 'c.1.2' or \$sf2 eq 'c.1.3' or \$sf2 eq 'c.1.4' or \$sf2 eq 'c.1.5' or \$sf2 eq 'c.1.6' or \$sf2 eq 'c.1.7')){
\$flag=1;
}
elsif ((\$cf1 eq 'c.1' and \$cf2 eq 'c.1' and (\$sf1 ne \$sf2))){
\$flag=0;
}

#Rossmann-like
if (exists(\$rossmann{\$cf1}) and exists(\$rossmann{\$cf2})){
if (\$cf1 eq \$cf2){
\$flag=1;
}
else{
\$flag=0;
}
}
#Nah! Julian thinks now it's a grower, since 1.63
##as of 1.57  c.23.12 looks like superposes OK
#if ((exists(\$rossmann{\$cf1}) and \$sf2 eq 'c.23.12') or (exists(\$rossmann{\$cf2}) and \$sf1 eq 'c.23.12')){
#\$flag=1;
#}
#Old note -correspondance checked-
#1ykf, residues 151-314 superpose with 1eiz: 2.26382 ANGSTROMS/ATOM over 98 residues
if ((exists(\$rossmann{\$cf1}) and \$cf2 eq 'c.66') or (exists(\$rossmann{\$cf2}) and \$cf1 eq 'c.66')){
\$flag=0;
}
#1lvh superposes with 1ek6 to 2.19488 ANGSTROMS/ATOM over 88 residues(same topology), BUT is VERY different
if ((exists(\$rossmann{\$cf1}) and \$cf2 eq 'c.108') or (exists(\$rossmann{\$cf2}) and \$cf1 eq 'c.108')){
\$flag=0;
}
#Can't find it and there are no cross-hits anyway.
##Old note -correspondance checked-
#if ((exists(\$rossmann{\$cf1}) and \$cf2 eq 'c.32') or (exists(\$rossmann{\$cf2}) and \$cf1 eq 'c.32')){
#\$flag=0;
#}
#note: the ATP nucleotide-binding site is similar to that of the NAD-binding Rossmann-folds
if ((exists(\$rossmann{\$cf1}) and \$sf2 eq 'c.111.1') or (exists(\$rossmann{\$cf2}) and \$sf1 eq 'c.111.1')){
\$flag=0;
}

#Other rules
if ((\$cf1 eq 'b.66' or \$cf1 eq 'b.67' or \$cf1 eq 'b.68' or \$cf1 eq 'b.69' or \$cf1 eq 'b.70') and (\$cf2 eq 'b.66' or \$cf2 eq 'b.67' or \$cf2 eq 'b.68' or \$cf2 eq 'b.69' or \$cf2 eq 'b.70')){
if (\$cf1 eq \$cf2){
\$flag=1;
}
else{
\$flag=0;
}
}
#Note in SCOP, Similar in architecture but partly differs in topology Periplasmic binding protein-like I/II
if ((\$cf1 eq 'c.94' and \$cf2 eq 'c.93') or( \$cf2 eq 'c.94' and \$cf1 eq 'c.93')){
\$flag=0;
}
#This re-classified in 1.67 (Cutinase-like)
#if ((\$sf1 eq 'c.23.9' and \$sf2 eq 'c.69.1') or (\$sf2 eq 'c.23.9' and \$sf1 eq 'c.69.1')){
#\$flag=0;
#}
#This re-classified in 1.63
#if ((\$fa1 eq 'f.2.1.10' and \$sf2 eq 'c.108.1') or (\$fa2 eq 'f.2.1.10' and \$sf1 eq 'c.108.1')){
#\$flag=1;
#}
#Very similar alpha super-helix
if ((\$sf1 eq 'a.118.8' and \$sf2 eq 'a.118.6') or (\$sf2 eq 'a.118.8' and \$sf1 eq 'a.118.6')){
\$flag=0;
}
#Similar motif sulphur binding
if ((\$sf1 eq 'd.58.1' and \$sf2 eq 'a.1.2') or (\$sf2 eq 'd.58.1' and \$sf1 eq 'a.1.2')){
\$flag=0;
}
#OK note in SCOP one of the previous cases
if ((\$sf1 eq 'a.137.4' and \$sf2 eq 'c.96.1') or (\$sf2 eq 'a.137.4' and \$sf1 eq 'c.96.1')){
\$flag=0;
}
#OK same fold and general look
if ((\$sf1 eq 'b.42.5' and \$sf2 eq 'b.42.1') or (\$sf2 eq 'b.42.5' and \$sf1 eq 'b.42.1')){
\$flag=0;
}
#Note in SCOP. Leucine rich repeats both of them,  structures look the same OK
if ((\$sf1 eq 'c.10.1' and \$sf2 eq 'c.10.2') or (\$sf2 eq 'c.10.1' and \$sf1 eq 'c.10.2')){
\$flag=0;
}
##re-classified in SCOP 1.67
##Obvious sequence homology with blast,  one is beta-beta-alpha superhelix,  and one is beta-alpha togethor in PFAM
#if ((\$sf1 eq 'c.11.1' and \$sf2 eq 'c.10.2') or (\$sf2 eq 'c.11.1' and \$sf1 eq 'c.10.2')){
#\$flag=0;
#}
##Obvious sequence homology with blast,  one is beta-beta-alpha superhelix,  and one is beta-alpha togethor in PFAM
#if ((\$sf1 eq 'c.11.1' and \$sf2 eq 'c.10.1') or( \$sf2 eq 'c.11.1' and \$sf1 eq 'c.10.1')){
#\$flag=0;
#}
#Note in SCOP, contains P-loop
if ((\$sf1 eq 'c.91.1' and \$sf2 eq 'c.37.1') or( \$sf2 eq 'c.91.1' and \$sf1 eq 'c.37.1')){
\$flag=0;
}
#Note in SCOP, shared motif
if ((\$sf1 eq 'd.51.1' and \$sf2 eq 'd.52.3') or( \$sf2 eq 'd.51.1' and \$sf1 eq 'd.52.3')){
\$flag=0;
}
#Note in SCOP: variant of beta/alpha barrel
if ((\$cf1 eq 'c.6' and \$cf2 eq 'c.1') or( \$cf2 eq 'c.6' and \$cf1 eq 'c.1')){
\$flag=0;
}
if ((\$sf1 eq 'a.24.1' and \$sf2 eq 'a.63.1') or( \$sf2 eq 'a.24.1' and \$sf1 eq 'a.63.1')){
\$flag=0;
}

####NEw to 1.69
##Shared helix no note in SCOP, sequence identical, structure different position d1dkza1 hit d1bpr__ Seems to have been fixed (note)
#if ((\$sf1 eq 'a.8.4' and \$sf2 eq 'b.130.1') or( \$sf2 eq 'a.8.4' and \$sf1 eq 'b.130.1')){
#\$flag=0;
#}
#Shared helix no note in SCOP, sequence aligns, structure looks same (domain boundary definition problem) d1t3ta1 hit d1vk3a1
if ((\$sf1 eq 'a.5.10' and \$sf2 eq 'd.79.4') or( \$sf2 eq 'a.5.10' and \$sf1 eq 'd.79.4')){
\$flag=0;
}
#Shared helix no note in SCOP, sequence alignment very bad, but includes a hyper-variable linker region. Looks like a misclassified? part of a strange chain d1vf5b hit d1bccc3 # note in SCOP but not exactly clear if the note means this or something else
if ((\$sf1 eq 'f.21.1' and \$sf2 eq 'f.32.1') or( \$sf2 eq 'f.21.1' and \$sf1 eq 'f.32.1')){
\$flag=0;
}
###-----------

####NEw to 1.73
##Note in SCOP similar sequence repeat, but also similar assembly
if ((\$sf1 eq 'a.118.24' and \$sf2 eq 'd.211.1') or( \$sf2 eq 'a.118.24' and \$sf1 eq 'd.211.1')){
\$flag=0;
}
###------------

####NEw to coiled coils in 1.73 --based on comments made by Owen--
#Note in SCOP  for a.38.1 that reads "Contains a leuzine zipper motif" and the h.1.3 class is the leuzine zipper family.
if ((\$sf1 eq 'h.1.3' and \$sf2 eq 'a.38.1') or( \$sf2 eq 'h.1.3' and \$sf1 eq 'a.38.1')){
\$flag=0;
}
#There is a note in SCOP for a.24.1 that reads "Can exist in a coiled coil oligormeric state, see PDB entry 1av1" which is the pdb which is making the incorrect hit.
if ((\$sf1 eq 'h.5.1' and \$sf2 eq 'a.24.1') or( \$sf2 eq 'h.5.1' and \$sf1 eq 'a.24.1')){
\$flag=0;
}
#Note in SCOP: a globular structure of a larger fragment containing this region is available; (1dn1), chain B  where 1dn1 is in the a.47.2 class.
if ((\$sf1 eq 'h.1.15' and \$sf2 eq 'a.47.2') or( \$sf2 eq 'h.1.15' and \$sf1 eq 'a.47.2')){
\$flag=0;
}
#These are fusion proteins that have a unit from both the h.1.3 and h.3.2 proteins. Also int terms of straight forward yes/no coiled coil prediction it makes no real difference!
if ((\$sf1 eq 'h.1.3' and \$sf2 eq 'h.3.2') or( \$sf2 eq 'h.1.3' and \$sf1 eq 'h.3.2')){
\$flag=0;
}
###------------

####NEw to 1.75
##d2duya1 seems to hit d2i5ha1, gets structural hit with GANGSTA, superposes nicely with 2duy Alexey will probably change this in 1.77
if ((\$sf1 eq 'a.60.2' and \$sf2 eq 'e.71.1') or( \$sf2 eq 'a.60.2' and \$sf1 eq 'e.71.1')){
\$flag=0;
}
##note in SCOP: related to domain 3 of the Polypeptide chain release factors RF1 and RF2 (scop_fa 75621)
if ((\$sf1 eq 'e.38.1' and \$sf2 eq 'd.50.4') or( \$sf2 eq 'e.38.1' and \$sf1 eq 'd.50.4')){
\$flag=0;
}
##note in SCOP: The active site is formed by the toprim and "winged helix" domains (domains 1 and 4); these two domains are also found in the type II topoisomerase (DNA gyrase A) and in the alpha subunit of topoisomerase IV
if ((\$sf1 eq 'e.10.1' and \$sf2 eq 'a.4.5') or( \$sf2 eq 'e.10.1' and \$sf1 eq 'a.4.5')){
\$flag=0;
}
##note in SCOP: insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
if ((\$fa1 eq 'a.4.5.1' and \$sf2 eq 'g.41.5') or( \$fa2 eq 'a.4.5.1' and \$sf1 eq 'g.41.5')){
\$flag=0;
}
###------------

#-----------------------------------

return (\$flag);
}

```