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

Evaluating a set of protein structure predictions is difficult as each pred iction may omit different residues and different parts of the structure may have different accuracies. A method is described that captures the best re sults from a large number of alternative sequence-dependent structural supe rpositions between a prediction and the experimental structure and represen ts them as a single line on a graph. Applied to GASP2 and CASP3 data the be st predictions stand out visually in most cases, as judged by manual inspec tion. The results from this method applied to GASP data are available from the URLs http://PredictionCenter. Ilnl.gov/casp3/results/th/ and http://www .sanger. ac.uk/similar to th/casp/. (C) 1999 Wiley-Liss, Inc.