@@ -56,3 +56,20 @@ The steps are generally as follows:
* This program launches many Rosetta processes in parallel, each of which writes to its own output databases. When performing alanine scans over large numbers of residues and/or replicates, this leads to significant slowdowns in the analysis of the data, as each of the ddG output databases has to be opened and queried for data. Ideally, we would have multiple processes write output to a single shared database or set of shared databases, to reduce the need for many file I/O operations (which can be slow/incurs additional latency penalties, especially on compute cluster filesystems)
* Improvements can be made to looking at subsets of fibril residues for energetics calculations. Preliminary work has been done to support this, but analyzing e.g. only the center chains of a fibril stack to avoid edge effects or looking at the per-residue energies is not currently as easy as it could be.
* Refactor to pull all the common code between method variants into a shared library to reduce code duplication
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