HI FROM THE NYU CENTER FOR COMPARATIVE FUNCTIONAL GENOMICS!
ok, i'm a bit excited ...

HPF2 is launched. This is very exiting to me and to my lab members. We’ve been working with IBM for a while now and were very excited when they told us that we could put this project on the grid.

HPF2 is different from HPF1, but in a way that might not mean much to those who don’t think about structure prediction. HPF2 is a higher resolution version of HPF1. In HPF1 we modeled the protein at the level of overall shape (each part of the molecule was represented by a few atoms). In HPF2 we try to model all atoms in the protein and use a mode of Rosetta that pays attention to roughly twice the number of atoms modeled in HPF1. This means we have to spend more compute time per protein and that we have to narrow our focus for HPF2.

If you’re new to HPF then check out the FAQ for HPF2 and HPF1. There is a lot of information in the descriptions of HPF2 that refers back to HPF1 so check out the HPF1 faq and description first if your interested.

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more details:
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HPF phase II:

HPF phase-2 will refine, using Rosetta in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the Human Proteome Folding Project (HPF phase1). The project will focus on human secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the pro-teins). The project will also focus on key secreted pathogenic protein. This project dove-tails with efforts at the ISB in Seattle to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future).

This project continues where the Human Proteome Folding Project leaves off. With the Human proteome Folding project we aimed to get protein function. With the second phase we would aim to increase the resolution of a select subset of Human proteins. Better reso-lution is important for a number of applications including but not limited to virtual screening of drug targets with docking procedures and protein design. The second phase of the pro-ject will also serve to improve our understanding of the physics of protein structure and ad-vance the state of the art in protein structure prediction (help us to further develop our program, Rosetta).

The two main objectives are to: 1) obtain higher resolution structures for specific hu-man proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta structure prediction. Thus, the project would ad-dress two very important parallel imperatives, one biological and one biophysical.

The Human Proteome Folding Project Phase-2 will use the computer power of millions of computers to predict the shape of Human proteins for which researchers currently know little. From this detailed shape scientists hope to learn about the function of these proteins, as the shape of proteins is inherently related to how they function in our bodies. This data-base of protein structures and putative functions will let scientists take the next steps un-derstanding how diseases that involve these proteins work. Proteins are the most important molecules in living beings. Just about everything in your body involves or is made out of pro-teins. Protein structure is key to understanding the functions of this diverse class of bio-molecule. Thus we hope that our work on HPF 1 and HPF 2 will contribute to critical pub-lic infrastructure to the biological and biomedical community.