A hybrid algorithm for determining protein structure

At Thinking Machines, my colleagues and I have developed a hybrid system combining a neural network, a statistical module, and a memory-based reasoner, each of which makes its own prediction. A combiner then blends these results to produce the final predictions. This hybrid system improves its ability to determine how amino acid sequences fold into 3D protein structures. It predicts secondary structures with 66.4% accuracy. Both the neural network and the combiner are multilayer perceptrons trained with the standard backpropagation algorithm; this article focuses on the other two components, and on how we trained the hybrid system and used it for prediction. I also discuss how future work in AI and other sciences might meet the challenge of the protein folding problem.<>