Some measures of comparative performance in the three CASPs

Performance in the three Critical Assessment of protein Structure Predictio n (CASP) experiments has been compared in the areas of alignment accuracy f or models based on homology and three-dimensional accuracy for models produ ced by using ab initio prediction methods. The homologous models span the c omparative modeling and fold-recognition regimes. Each CASP target is assig ned a relative difficulty based on the extent of sequence identity and the degree of structural overlap with the best available template. There is a c lear improvement in alignment accuracy between CASP1 and CASPs 2 and 3 over much of the difficulty scale but no apparent improvement between CASP2 and CASP3. Encouragingly, the best ab initio models of small targets are clear ly more accurate in CASP3 than in CASPs 1 and 2. Published 1999 Wiley-Liss, Inc.dagger.