Assessment of progress over the CASP experiments

• Published in: Proteins, structure, function, and bioinformatics Vol. 53; no. S6; pp. 585 - 595
• Main Authors: Venclovas, C̆eslovas, Zemla, Adam, Fidelis, Krzysztof, Moult, John
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 2003
• Subjects: Algorithms; CASP; communitywide experiment; Computational Biology - methods; Protein Conformation; Protein Folding; protein structure prediction; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins - chemistry; Reproducibility of Results; Sensitivity and Specificity; Sequence Alignment - methods
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10530

The quality of structure models produced in the CASP5 experiment has been compared with that in earlier CASPs. The most significant progress is in the fold recognition regime, where the development of meta‐servers has allowed more accurate consensus models to be generated. In contrast to this, there is little evidence of progress in producing more accurate comparative models, particularly those based on sequence identities > 30%. For comparative models based on low‐sequence identity and for fold recognition models, accuracy depends primarily on the fraction of the target structure that is similar to an available template, and the quality of the alignment. Overall, these results indicate that there are still no effective methods of improving model quality beyond that obtained by successfully copying a template structure. For models of proteins with previously unknown folds, there appears to be a pause in the previous consistent improvement. There is some evidence that more groups are producing top‐quality models, however. Although specific progress between successive experiments is sometimes difficulty to identify, over the history of all the CASPs there has been steady, if sometimes slow, progress in all modeling regimes. Proteins 2003;53:585–595. © 2003 Wiley‐Liss, Inc.