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ModeRNA: a tool for comparative modeling of RNA 3D structure.

Rother M, Rother K, Puton T, Bujnicki JM - Nucleic Acids Res. (2011)

Bottom Line: It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family.It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry.Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul Ks Trojdena 4, 02-109 Warsaw, Poland.

ABSTRACT
RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.

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Evaluation of tRNA models generated from templates and alignments with (a) DI and (b) DP measures.
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Figure 4: Evaluation of tRNA models generated from templates and alignments with (a) DI and (b) DP measures.

Mentions: In our evaluation we also included the deformation index (DI) and the deformation profile (DP) measures recently introduced by Parisien et al. (48). The DI evaluates the conservation of base–base interactions (including stacking interactions and both canonical and non-canonical base pairing). The DP is a matrix of average distances, calculated by superimposing all nucleotides from model and the reference structure and then computing the average distance between each base from model and the corresponding base from the reference structure. For the set of tRNA models we obtained an average DI of 0.62 and an average DP of 13.82 (Figure 4). According to the histogram, the majority of models achieve a DI score in the range of 0.5–0.8. The low average is caused mainly by changes in intermolecular interaction patterns between tRNAs in different functional states (e.g. splaying out bases upon complex formation with protein partners). A more in-depth analysis of contact patterns in tRNA would be beneficial to improve this particular aspect. The distortion profile average and maximum values are higher than for the examples given in the article by Parisien et al. (48). The main reason for this are: (i) the DP score is size-dependent and tRNA molecules are larger than the mentioned examples and (ii) the conformation and interactions of residues in the anticodon loop and in the acceptor stem exhibit large variations (depending on the functional state and interactions with other macromolecules). When different structures are superimposed based on these residues, other residues can be displaced to generate global RMSD values up to 50 Å. Nevertheless, the majority of residues generate superpositions with RMSD values around 5 Å.Figure 4.


ModeRNA: a tool for comparative modeling of RNA 3D structure.

Rother M, Rother K, Puton T, Bujnicki JM - Nucleic Acids Res. (2011)

Evaluation of tRNA models generated from templates and alignments with (a) DI and (b) DP measures.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105415&req=5

Figure 4: Evaluation of tRNA models generated from templates and alignments with (a) DI and (b) DP measures.
Mentions: In our evaluation we also included the deformation index (DI) and the deformation profile (DP) measures recently introduced by Parisien et al. (48). The DI evaluates the conservation of base–base interactions (including stacking interactions and both canonical and non-canonical base pairing). The DP is a matrix of average distances, calculated by superimposing all nucleotides from model and the reference structure and then computing the average distance between each base from model and the corresponding base from the reference structure. For the set of tRNA models we obtained an average DI of 0.62 and an average DP of 13.82 (Figure 4). According to the histogram, the majority of models achieve a DI score in the range of 0.5–0.8. The low average is caused mainly by changes in intermolecular interaction patterns between tRNAs in different functional states (e.g. splaying out bases upon complex formation with protein partners). A more in-depth analysis of contact patterns in tRNA would be beneficial to improve this particular aspect. The distortion profile average and maximum values are higher than for the examples given in the article by Parisien et al. (48). The main reason for this are: (i) the DP score is size-dependent and tRNA molecules are larger than the mentioned examples and (ii) the conformation and interactions of residues in the anticodon loop and in the acceptor stem exhibit large variations (depending on the functional state and interactions with other macromolecules). When different structures are superimposed based on these residues, other residues can be displaced to generate global RMSD values up to 50 Å. Nevertheless, the majority of residues generate superpositions with RMSD values around 5 Å.Figure 4.

Bottom Line: It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family.It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry.Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul Ks Trojdena 4, 02-109 Warsaw, Poland.

ABSTRACT
RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available.

Show MeSH