We'll be uploading more work units to IBM soon; there's no concern. We also have a batch mp 200-999 that was initially skipped. So we've bought a few more weeks, and are working towards the next experiment. Some of the analysis we've performed for the paper-in-progress has inspired new ideas.

To answer rilian, we have already run about 100 different species through the HPF pipeline. The unifying factor is that all of these organisms provoke particular interest in the scientific community. Many are parasites and disease causing species that affect humans, some are important for studying human food sources, etc. It's safe to say that rice is one of the most important food sources for humans, if not the most heavily consumed food source. Improving annotation of the rice proteome, as well as the other organisms we've folded, greatly increases the available scientific resources for researchers studying any of these species.

As for folding all of the human proteome... There are somewhere around 30k protein coding regions, of which we identified near 70k uniquely folding protein domains. Many of these can be matched to known protein structures, above 50%, using sequence based similarity methods. We've folded thousands on the WCG, but not everything. Rosetta's effectiveness diminishes due to a number of factors including, but not limited to, protein length, disorder, and trans-membrane regions. We've already run everything that passed our filters.

pcw216
thank you for clarification!

Interesting - may I ask what that was? I cannot find these in your experiments table...

Regards,
Martin

The first 200 mp's were actually part of a small experiment we ran to benchmark HPF2. In Superfamily assignments for the yeast proteom...n with the gene ontology., using the original HPF1 pipeline, we used Rosetta to fold a thousand proteins with known structure. We folded these again with HPF2's increased sample size and all atom mode to compare to the original models.

Any news here?
I am chrunching mp 211 right now.