I think AlphaGo is a fundamentally different problem than is the protein folding problem. I can generate a Go board and a sequence of strictly valid moves becau

I think AlphaGo is a fundamentally different problem than is the protein folding problem. I can generate a Go board and a sequence of strictly valid moves because I know the rules for Go. With certain limited high level exceptions (like the sequence is linear, you can't have bond angles of a certain degree etc.) those rules don't exist as such for protein folding. In other words if I generate 1000 protein folds, I don't know which ones are physically valid. That's a problem for the kind of iteration I think you're describing, though I may be misunderstanding. Another way of seeing this limitation is that we have great models for predicting what the weather will be like a few days from now, almost down the hour. But when asked to predict whether it will snow a month from now, we can't. That's because highly accurate models on small scale timescales become too noisy on longer timescales. In protein folding, just s/timescale/sequence length/.