This paper presents results of an all-sky searches for periodic gravitational waves in the frequency range $[50, 1190] \text{ Hz}$ and with frequency derivative ranges of $\sim[-2 \times 10^{-9}, 1.1 \times 10^{-10}] \text{ Hz}/s$ for the fifth LIGO science run (S5). The novelty of the search lies in the use of a non-coherent technique based on the Hough-transform to combine the information from coherent searches on timescales of about one day. Because these searches are very computationally intensive, they have been deployed on the Einstein@Home distributed computing project infrastructure. The search presented here is about a factor 3 more sensitive than the previous Einstein@Home search in early S5 LIGO data. The post-processing has left us with eight surviving candidates. We show that deeper follow-up studies rule each of them out. Hence, since no statistically significant gravitational wave signals have been detected, we report upper limits on the intrinsic gravitational wave amplitude $h_0$. For example, in the 0.5 Hz-wide band at 152.5 Hz, we can exclude the presence of signals with $h_0$ greater than $7.6 \times 10^{-25}$ with a 90% confidence level.