Compiling keywords can make a difference if you do all of them at once, before the loop.

#!/usr/bin/perl -w
use strict;

open WORDS, "<kwords" or die;
my %kwords=();
while (<WORDS>) {
    chomp;
    $kwords{$_} = qr/\b$_\b/m;
}
close WORDS;

my %found =();

for my $f (<abstract*>) {
    local $/;
    open FILE, $f or die "$f\n";
    my $text = <FILE>;
    close FILE;
    for (keys %kwords) {
        my $val = $kwords{$_};
        $found{$f} .= "$_ " if $text =~ /$val/;
    }
}

print "$_\t$found{$_}\n" for sort keys %found;
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Assuming that the keywords are in a file, and each abstract is in a separate file, precompilation makes the search 30% faster (using 1000 test files, 300 words each, 3 random keywords in 2/3 of them).