Journal article
Assessment of protein structure refinement in CASP9
Proteins, structure, function, and bioinformatics, Vol.79(Suppl 10), pp.74-90
2011
DOI: 10.1002/prot.23131
PMCID: PMC3238793
PMID: 22069034
Abstract
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 to 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.
Details
- Title: Subtitle
- Assessment of protein structure refinement in CASP9
- Creators
- Justin L MacCallum - Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityAlberto Perez - Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityMichael J Schnieders - Department of Biomedical Engineering, University of Texas at AustinLan Hua - Department of Pharmaceutical Chemistry, University of California San FranciscoMatthew P Jacobson - Department of Pharmaceutical Chemistry, University of California San FranciscoKen A Dill - Laufer Center for Physical and Quantitative Biology, Stony Brook University
- Resource Type
- Journal article
- Publication Details
- Proteins, structure, function, and bioinformatics, Vol.79(Suppl 10), pp.74-90
- DOI
- 10.1002/prot.23131
- PMID
- 22069034
- PMCID
- PMC3238793
- NLM abbreviation
- Proteins
- ISSN
- 0887-3585
- eISSN
- 1097-0134
- Grant note
- R01 GM081710-03 || GM / National Institute of General Medical Sciences : NIGMS R01 GM090205-03 || GM / National Institute of General Medical Sciences : NIGMS
- Language
- English
- Date published
- 2011
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024517302771
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