Are there known dimensional measurements for the classification of folded proteins given a starting chunk/domain as defined by something like the clustering functionality of MSM Builder?
Examples of what I would be looking for would be dimensions such as:
Reducing Agent Concentration
With corresponding scales and precisions such as:
logorithmic vs linear
distribution (e.g. dissolved/flat vs fractal/inclusions)
The above parameters would be included in folding software after a known starting conformation provided by MSM Builder or similar chunking software to derive a GUID for proteins without (or with extremely minimal and tuneable) collisions?
For instance, if hundreds of GUIDs on average end up equating to the same folded protein that's fine, but if one GUID could map to two or more thermodynamically stable folded proteins at greater than some incredibly small (e.g. 0.0000001%) then it wouldn't fit what I'm looking for. I know this is inherently NP-hard, but the complete ID would be something like:
So I would expect the chunkId and dimensional parameters to play a significant role in reducing collisions for different starting parameters.
It's worth noting I'm not seeking some magic bullet where you type an ID and get a fully folded protein, just a reliable system of GUIDs with enough starting information embedded in the ID to start the folding process.