my ( $R_score, @protein, @R_score_protein );

##</code><code>##

my ( @protein, @R_score_protein );
...
push( @R_score_protein, $1 );

##</code><code>##

use Getopt::Long;
our URL = "http://www.bork.embl-heidelberg.de/g2d/"
    .     "list_hits_disease.pl?U57042:Inflammatory_bowel_disease_7";

GetOptions( 'url=s', \$URL ) || die ( "Error reading command line args" );
my $browser = LWP::UserAgent->new();
my $resp = $browser->get( $URL );

##</code><code>##

while ( $content_all =~ m{R\-score<\/A>\s=\s(\d\.\d+)\;}g ) {
    push( @R_score_protein, $1 );
}
while ( $content_all =~ m{\[(NP_\d+)\]}g ) {
    push @protein, $1;
}

##</code><code>##

my $protein_re = qr|\[(NP_\d+)\]|;
my $score_re = qr|R-score</A>\s=\s(\d\.\d+)|;
while ( $content_all =~ m{$protein_re} ) .....
while ( $content_all =~ m{$score_re} ) ....

##</code><code>##

# $record stores references to hashes, 
# which are accumulated in @records
#
my ($record, @records);
for my $line ( break_into_lines( $resp->content() ) ) {
    if ( $line =~ /CANDIDATE/ ) {
        #
        # Save previous record, if there is one
        #
        if ( defined $record ) {
            push( @records, $record ); 
        }
        $records = {};                 # assign a new anon. hash.
    }
    # In the hash referenced by $record, use the 'protein' key
    # to access an array into which the $protein is/are added.
    #
    while ( my ( $protein ) = ( $line =~ /$protein_re/g ) ) {
        push( @{ $record->{'protein'} }, $protein );
    }
    if ( my ( $score ) = ( $line =~ /$score_re/g ) ) {
        push( @{ $record->{'score'} }, $score );
    }
}

##</code><code>##

for my $records ( @records ) {
    print "Proteins: ", join( ", ", @{ $record->{'protein'} } ), "\n" 
       if ( scalar @{ $record->{'protein'} } );
    print "Score: ", $record->{'score'}, "\n";
    print "-" x 72;
}