How about a lookahead assertion and the perl5.10 (*FAIL) pattern to find all matches :-)

 perl -e '$_="YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDK"; /N(?=\
+[115\])(?{print pos, "\n"})(*FAIL)/'
13
36
[download]

See perlre for more information.