Inverted protein structure prediction

Today we know of over 1000 protein structures, which can be classified into approximately 120 distinct folding patterns. The database of known structures provides numerous examples of proteins that adopt very similar folds, with some in each folding class having similar sequences. But there are also examples of proteins with similar structures that share no obvious sequence similarity. Thus among the 60000 known amino acid sequences, there must be many that adopt the 120 known folds but cannot be identified based on sequence relationships alone. It is the goal of inverted protein structure prediction to determine whether an amino acid sequence adopts a known structure. Here, we review the recent, rapid progress in inverted structure prediction. The power of this new generation of methods is that, instead of looking for similarity in sequences, they attempt to match one-dimensional sequences directly to three-dimensional folds.