New Projects (p6313-6316) for uniprocessor client

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Vincent Voelz has just put online a new set of projects for the Folding@Home uniprocessor client (single processor). These projects require the "Big WUs" setting to be set, and their value is doubled compared to the usual benchmark. Each unit reported 336 points and should preferably be returned within 36 days, and no later than 52 days.

The SH3 domain is a molelcule found throughout many diverse biological systems. It is usually part of a larger complex that helps to integrate a cellular signals. Its main function is modulate and regulate signaling by transiently binding a certain class of polyproline motifs. The specificty of different forms of SH3 for certain peptide motifs can vary widely, and great insights into celluar signaling networks could be gained by computational prediction of sequence-dependent affiities.

These are simulations designed to test a new sampling method that we have been developing, called the multi-scale fragment potential (MSFP) method. In MSFP, the problem of computing how a peptide chain binds to a receptor surface is broken down into parts that can be efficiently parallelized. Instead of simulating the interaction between a large polypeptide chain and a receptor, we break the peptide chain into small fragments, and exhaustively scan the receptor surface to construct a potential of mean force for each fragment. Using this detailed chemical information, we then use a coarse-grained chain model to sample peptide conformation and sequence space.

The simulations in these projects are of single-amino fragments anchored along the surface of test protein, Abl SH3 domain. These tests will let us test some of the fundamental assumptions of the MSFP method.

Points and deadlines:

  • project 6313: 336 points, timeout 36 days, deadline 52 days
  • project 6314: 336 points, timeout 36 days, deadline 52 days
  • project 6315: 336 points, timeout 36 days, deadline 52 days
  • project 6316: 336 points, timeout 36 days, deadline 52 days

(NOTE: Because these are large WUs (>5 MB), the statcredit point value is doubled from the value obtained by our standard benchmarking scheme).

Information gathered from the project description