#!/usr/bin/perl

while(<>){
  /^<name>.*<\/name>/ or next;
  $_ =~ s/<name>//;
  $_ =~ s/<\/name>//;
  print $_;
}

#Run this by typing
#   perl list.pl protein.txt
#at the command prompt.
#Alternatively, 
#  ./list.pl protein.txt
#will work if list.pl is executable.

#The while(<>) automatically processes whatever
#file is supplied at the command line.

#The line:
#  /^<name>.*<\/name>/ or next;
#simply skips all lines that don't match
#that pattern.