RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions.

Evaluating a set of protein structure predictions is difficult as each prediction may omit different residues and different parts of the structure may have different accuracies. A method is described that captures the best results from a large number of alternative sequence-dependent structural superpositions between a prediction and the experimental structure and represents them as a single line on a graph. Applied to CASP2 and CASP3 data the best predictions stand out visually in most cases, as judged by manual inspection. The results from this method applied to CASP data are available from the URLs http:/(/)PredictionCenter. llnl.gov/casp3/results/th/ and http:/(/)www.sanger.ac.uk/ approximately th/casp/.