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Hmm, I can think of a few projects building protein structures through inference / homology models / multiple sequence alignments, but most of this I haven't given any serious thought to in years. This might be of interest to you (There's a bunch of papers from the same group along the same lines), but it's more from the perspective of looking at structural evolution through physical models (Modeling the energetic changes in "evolutionary space"), rather than any sort of machine-learning approach. X-ray crystallography in undergrad.Do you work on folding?