New metrics for comparing and assessing discrepancies between RNA 3D structures and models
- 26 August 2009
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 15 (10), 1875-1885
- https://doi.org/10.1261/rna.1700409
Abstract
To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base–base-stacking and base–base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between structures at the nucleotide scale for both intradomain and interdomain interactions. Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.Keywords
This publication has 37 references indexed in Scilit:
- Frequency and isostericity of RNA base pairsNucleic Acids Research, 2009
- Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filtersRNA, 2009
- Annotation of tertiary interactions in RNA structures reveals variations and correlationsRNA, 2008
- Automated motif extraction and classification in RNA tertiary structuresRNA, 2008
- Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS dataJournal of Biomolecular NMR, 2008
- Progress and challenges in protein structure predictionCurrent Opinion in Structural Biology, 2008
- Automated de novo prediction of native-like RNA tertiary structuresProceedings of the National Academy of Sciences of the United States of America, 2007
- Modeling RNA tertiary structure motifs by graph-grammarsNucleic Acids Research, 2007
- The interaction networks of structured RNAsNucleic Acids Research, 2006
- Automated extraction and classification of RNA tertiary structure cyclic motifsNucleic Acids Research, 2006