Automated large scale evaluation of protein structure predictions

Evaluation and assessment are methods might work could not be reached. On t he basis of critical issues in GASP experiments. Automated procedures are n ecessary to compare a large number of predictions with the target folds. Th e evaluation has to reveal the maximum extent of similarity between predict ions and targets, it should be applicable across prediction categories, and it should be transparent and accessible to a wide community. Here we prese nt an automated evaluation scheme which is an attempt to meet these require ments. In the implementation and execution of this scheme we had to solve o r circumvent problems of convergence, where algorithms fail to find optimum solutions, problems of ambiguity where no unique optimum solution exists, and problems in ranking and interpretation. Key features of this implementa tion are (1) the root mean square deviation of structure superimposition is kept close to a constant value throughout the evaluation and (2) all struc tural matches found between two folds are taken into account. We discuss th ese points in detail and describe the numerical criteria used in the CASP3 evaluation. (C) 1999 Wiley-Liss, Inc.