The authors state no conflict of interest.
Assessment of protein structure refinement in CASP9†
Article first published online: 30 AUG 2011
Copyright © 2011 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 79, Issue Supplement S10, pages 74–90, 2011
How to Cite
MacCallum, J. L., Pérez, A., Schnieders, M. J., Hua, L., Jacobson, M. P. and Dill, K. A. (2011), Assessment of protein structure refinement in CASP9. Proteins, 79: 74–90. doi: 10.1002/prot.23131
- Issue published online: 9 NOV 2011
- Article first published online: 30 AUG 2011
- Accepted manuscript online: 25 JUL 2011 11:13AM EST
- Manuscript Accepted: 3 JUL 2011
- Manuscript Revised: 15 JUN 2011
- Manuscript Received: 31 MAR 2011
- NIH. Grant Numbers: GM090205, GM34993, GM081210
- EMBO. Grant Number: ALTF 1107-2009 (Felloship).
- Structure prediction;
We assess performance in the structure refinement category in CASP9. Two years after CASP8, the performance of the best groups has not improved. There are few groups that improve any of our assessment scores with statistical significance. Some predictors, however, are able to consistently improve the physicality of the models. Although we cannot identify any clear bottleneck in improving refinement, several points arise: (1) The refinement portion of CASP has too few targets to make many statistically meaningful conclusions. (2) Predictors are usually very conservative, limiting the possibility of large improvements in models. (3) No group is actually able to correctly rank their five submissions—indicating that potentially better models may be discarded. (4) Different sampling strategies work better for different refinement problems; there is no single strategy that works on all targets. In general, conservative strategies do better, while the greatest improvements come from more adventurous sampling—at the cost of consistency. Comparison with experimental data reveals aspects not captured by comparison to a single structure. In particular, we show that improvement in backbone geometry does not always mean better agreement with experimental data. Finally, we demonstrate that even given the current challenges facing refinement, the refined models are useful for solving the crystallographic phase problem through molecular replacement. Proteins 2011;. © 2011 Wiley-Liss, Inc.