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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—relation between the sequence identity and (a) the GDT_TS score, (b) all atom RMSD of models against experimentally solved structures, (c) the P atom and the C4′ atom RMSD of models against experimentally solved structures (in black) and experimentally solved structures (templates) against experimentally solved structures (targets) (in red) and (d) all atom RMSD of models against experimentally solved structures where the anticodon and the CCA regions are excluded.
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Figure 2: Evaluation of tRNA models generated from templates and alignments—relation between the sequence identity and (a) the GDT_TS score, (b) all atom RMSD of models against experimentally solved structures, (c) the P atom and the C4′ atom RMSD of models against experimentally solved structures (in black) and experimentally solved structures (templates) against experimentally solved structures (targets) (in red) and (d) all atom RMSD of models against experimentally solved structures where the anticodon and the CCA regions are excluded.

Mentions: In order to provide a reasonable evaluation of our tRNA models, the Global Distance Test—Total Score (GDT_TS) was calculated, as it is widely used for the evaluation of protein models (46). The GDT_TS score denotes the sum of percent of residues that are within the 1, 2, 4 and 8 Å sphere between a superimposed model and native reference structure, divided by 4. The result can vary from 0 to 1 where a higher value denotes a more accurate model. The distance between two residues was calculated as the average of distances between the corresponding P and C4′ atoms (template versus model). In case of the 9675 tRNA models built by ModeRNA, the average GDT_TS value was equal to 0.5. The detailed results are shown in Figure 2.Figure 2.


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—relation between the sequence identity and (a) the GDT_TS score, (b) all atom RMSD of models against experimentally solved structures, (c) the P atom and the C4′ atom RMSD of models against experimentally solved structures (in black) and experimentally solved structures (templates) against experimentally solved structures (targets) (in red) and (d) all atom RMSD of models against experimentally solved structures where the anticodon and the CCA regions are excluded.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Evaluation of tRNA models generated from templates and alignments—relation between the sequence identity and (a) the GDT_TS score, (b) all atom RMSD of models against experimentally solved structures, (c) the P atom and the C4′ atom RMSD of models against experimentally solved structures (in black) and experimentally solved structures (templates) against experimentally solved structures (targets) (in red) and (d) all atom RMSD of models against experimentally solved structures where the anticodon and the CCA regions are excluded.
Mentions: In order to provide a reasonable evaluation of our tRNA models, the Global Distance Test—Total Score (GDT_TS) was calculated, as it is widely used for the evaluation of protein models (46). The GDT_TS score denotes the sum of percent of residues that are within the 1, 2, 4 and 8 Å sphere between a superimposed model and native reference structure, divided by 4. The result can vary from 0 to 1 where a higher value denotes a more accurate model. The distance between two residues was calculated as the average of distances between the corresponding P and C4′ atoms (template versus model). In case of the 9675 tRNA models built by ModeRNA, the average GDT_TS value was equal to 0.5. The detailed results are shown in Figure 2.Figure 2.

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