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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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Distances used in the pre-filtering stage of the fragment search.
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Figure 1: Distances used in the pre-filtering stage of the fragment search.

Mentions: For each indel, ModeRNA attempts to identify a backbone fragment with an appropriate length and superimposes its flanking residues onto the corresponding anchoring residues in the template structure as to maximize its fit to the anchor and to minimize steric clashes with the rest of the molecule. The fragment search includes a pre-filtering stage, where the geometry of the flanking residues is compared to all fragments of appropriate length from a library, and a fitting stage where the 50 most promising candidates are evaluated by inserting them into the model. If the gap cannot be closed by the above-mentioned procedure, e.g. if an extended fragment of the template is to be deleted and the resulting ends are too far from each other, ModeRNA will generate a model with an unsealed gap, and generate a warning that the model is discontinuous. Such situations often occur when modeling is attempted for a wrong template or in regions where the target–template alignment is erroneous. In the pre-filtering stage of the fragment search, the geometrical fit between the two flanking residues from the 5′-end (r5) and from the 3′-end (r3) is sought with the terminal nucleotides of each fragment of appropriate length in the library. The geometrical fit is evaluated by comparing six atom–atom distances (O5′r5–O5′r3, C5′r5–C5′r3, C4′r5–C4′r3, C3′r5–C3′r3, C1′r5–C1′r3, N1r5/N9r5–N1r3/N9r3)—see Figure 1. The sum of the square deviations of these values between the fragment ends and the flanking sites in the model roughly approximates the RMSD, and can be calculated rapidly for a huge number of candidate fragments.Figure 1.


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

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

Distances used in the pre-filtering stage of the fragment search.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Distances used in the pre-filtering stage of the fragment search.
Mentions: For each indel, ModeRNA attempts to identify a backbone fragment with an appropriate length and superimposes its flanking residues onto the corresponding anchoring residues in the template structure as to maximize its fit to the anchor and to minimize steric clashes with the rest of the molecule. The fragment search includes a pre-filtering stage, where the geometry of the flanking residues is compared to all fragments of appropriate length from a library, and a fitting stage where the 50 most promising candidates are evaluated by inserting them into the model. If the gap cannot be closed by the above-mentioned procedure, e.g. if an extended fragment of the template is to be deleted and the resulting ends are too far from each other, ModeRNA will generate a model with an unsealed gap, and generate a warning that the model is discontinuous. Such situations often occur when modeling is attempted for a wrong template or in regions where the target–template alignment is erroneous. In the pre-filtering stage of the fragment search, the geometrical fit between the two flanking residues from the 5′-end (r5) and from the 3′-end (r3) is sought with the terminal nucleotides of each fragment of appropriate length in the library. The geometrical fit is evaluated by comparing six atom–atom distances (O5′r5–O5′r3, C5′r5–C5′r3, C4′r5–C4′r3, C3′r5–C3′r3, C1′r5–C1′r3, N1r5/N9r5–N1r3/N9r3)—see Figure 1. The sum of the square deviations of these values between the fragment ends and the flanking sites in the model roughly approximates the RMSD, and can be calculated rapidly for a huge number of candidate fragments.Figure 1.

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