Structure Prediction Protein Design Biclustering + cMonkey Network Inference Publications          Links + Collaborations People                   Opportunities             Software + Code Teaching            


WCG Status Update

WCG Post

HPF2 Update - October 2010


As previously mentioned, we've been excited about folding a new set of proteins that brings the HPF project back to focusing on efforts directly related to human health. In the pursuit of basic research, we strive to fold a broad category of proteins from all branches of the tree of life. Nonetheless, the primary focus for the biological sciences should be the improvement of human health and wellbeing. We believe our new set of targets successfully resolves this dichotomy. We've begun folding novel proteins from the Human Microbiome Project's collection. It's widely believed that microbial cells in the human body outnumber our own by 10 to 1. The cooperation of non-pathogenic bacteria in the gut, for example, help us perform essential activities like digestion and nutrient absorption. They are widely believed to impact human health, having verified effects on such problems as the obesity epidemic. Future research in the area will inevitably lead to a better understanding of human health, and we are excited to be able to offer cutting edge predictions to the community.

In regards to our goal of diversity of sequences and genomes we fold on the World Community Grid, the HMP provides sequencing from hundreds of bacterial specimens. We are currently adding over 30,000 proteins into the HPF pipeline, all of which are novel with regards to protein structure prediction and have been identified in the human microbiome. Traditionally, the HPF pipeline and the Rosetta protocol perform best with small protein sequences (common in bacterial proteomes), and we expect to have relatively high yields of confident structure predictions that are applicable to human health. We should be folding the microbiome sequences for some time, on the order of months.

Please dig around and learn about the exciting project and its impact on the biological research community; it'ss truly fascinating.

A catalog of reference genomes from the human microbiome.
Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D.
Science. 2010 May 21;328(5981):994-9.

The Human Microbiome Project (HMP) Overview

The HMP Data Analysis and Coordination Center (DACC)