Limits...
ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.

Waleń T, Chojnowski G, Gierski P, Bujnicki JM - Nucleic Acids Res. (2014)

Bottom Line: Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base-phosphate and base-ribose interactions.The classifier can be easily extended to include new types of spatial relationships between pairs or larger assemblies of nucleotide residues.ClaRNA is freely available via a web server that includes an extensive set of tools for processing and visualizing structural information about RNA molecules.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland iamb@genesilico.pl.

Show MeSH
Additional classes of spatial relations between ribonucleotide residues detected and reported by ClaRNA: diagonal (consecutive) (A), diagonal (non-consecutive), arrows indicate main chain direction (B), sandwich (consecutive) (C) and base–ribose stacking (D). The pair of residues forming a contact is indicated by the green color, and possible neighboring residues are indicated by the gray color.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4231730&req=5

Figure 4: Additional classes of spatial relations between ribonucleotide residues detected and reported by ClaRNA: diagonal (consecutive) (A), diagonal (non-consecutive), arrows indicate main chain direction (B), sandwich (consecutive) (C) and base–ribose stacking (D). The pair of residues forming a contact is indicated by the green color, and possible neighboring residues are indicated by the gray color.

Mentions: In addition to the annotation of contact types, for which we prepared reference data sets based on RNA structure annotation by other methods, we trained ClaRNA to recognize several other types of spatial relations between adjacent residues that have a substantial number of occurrences in the analyzed RNA structures and in our subjective opinion are important for a clear understanding of RNA 3D architectures. The current version of ClaRNA reports four additional classes of relations, including direct base–ribose stacking, and three types of indirect relations that involve stacking and base pairing with other residues (Figure 4). In our experience, the detection of these relations can greatly facilitate the inference of secondary structure from 3D coordinates.


ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.

Waleń T, Chojnowski G, Gierski P, Bujnicki JM - Nucleic Acids Res. (2014)

Additional classes of spatial relations between ribonucleotide residues detected and reported by ClaRNA: diagonal (consecutive) (A), diagonal (non-consecutive), arrows indicate main chain direction (B), sandwich (consecutive) (C) and base–ribose stacking (D). The pair of residues forming a contact is indicated by the green color, and possible neighboring residues are indicated by the gray color.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231730&req=5

Figure 4: Additional classes of spatial relations between ribonucleotide residues detected and reported by ClaRNA: diagonal (consecutive) (A), diagonal (non-consecutive), arrows indicate main chain direction (B), sandwich (consecutive) (C) and base–ribose stacking (D). The pair of residues forming a contact is indicated by the green color, and possible neighboring residues are indicated by the gray color.
Mentions: In addition to the annotation of contact types, for which we prepared reference data sets based on RNA structure annotation by other methods, we trained ClaRNA to recognize several other types of spatial relations between adjacent residues that have a substantial number of occurrences in the analyzed RNA structures and in our subjective opinion are important for a clear understanding of RNA 3D architectures. The current version of ClaRNA reports four additional classes of relations, including direct base–ribose stacking, and three types of indirect relations that involve stacking and base pairing with other residues (Figure 4). In our experience, the detection of these relations can greatly facilitate the inference of secondary structure from 3D coordinates.

Bottom Line: Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base-phosphate and base-ribose interactions.The classifier can be easily extended to include new types of spatial relationships between pairs or larger assemblies of nucleotide residues.ClaRNA is freely available via a web server that includes an extensive set of tools for processing and visualizing structural information about RNA molecules.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland iamb@genesilico.pl.

Show MeSH