Fig. 2. : Optimal weights. The hydrogen bond threshold of each DSSP version used to construct DSSPcont is plotted versus the weight given. (a) The 100 best scoring (lowest average difference) weighting schemes of an extensive grid-search performed on 10 proteins are shown. Their apparent similarity indicates a well-defined global optimum. (b) We determined the optimal set of weights for DSSPcont using the entire set of 211 proteins through a stepwise gradient descent. Weights optimal for randomly chosen subsets of the 211 proteins were similar, i.e. the optimal set of weights was robust.