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FRASS: the web-server for RNA structural comparison.

Kirillova S, Tosatto SC, Carugo O - BMC Bioinformatics (2010)

Bottom Line: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank.Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Structural and Computational Biology, Max F Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria. sviatlana.kirylava@univie.ac.at

ABSTRACT

Background: The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.

Results: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.

Conclusions: The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

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Related in: MedlinePlus

Relationship between Gauss-integrals distances and ARTS and LaJolla scores. (A) Average values of the ARTS scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 820,600 pairs of RNA chains. (B) Average values of the LaJolla TM scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 5,050 pairs of tRNA chains. The dashed lines represent non-linear exponential curve fitting performed by GRACE program [30] with correlation coefficient -0.98.
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Figure 4: Relationship between Gauss-integrals distances and ARTS and LaJolla scores. (A) Average values of the ARTS scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 820,600 pairs of RNA chains. (B) Average values of the LaJolla TM scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 5,050 pairs of tRNA chains. The dashed lines represent non-linear exponential curve fitting performed by GRACE program [30] with correlation coefficient -0.98.

Mentions: The Gauss-integrals based algorithm was benchmarked against the ARTS method by using all RNA structures that were suitable for ARTS, which does not process single chain molecules that lack base pairs. The correlation between the Gauss-integrals based distances and the ARTS similarity scores was analyzed. Figure 4A shows the relationship between the ARTS scores and the Gauss-integrals Euclidean distances. This relationship, determined on the basis of 820,600 pairs of RNA chains, can be fitted by the exponential curve


FRASS: the web-server for RNA structural comparison.

Kirillova S, Tosatto SC, Carugo O - BMC Bioinformatics (2010)

Relationship between Gauss-integrals distances and ARTS and LaJolla scores. (A) Average values of the ARTS scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 820,600 pairs of RNA chains. (B) Average values of the LaJolla TM scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 5,050 pairs of tRNA chains. The dashed lines represent non-linear exponential curve fitting performed by GRACE program [30] with correlation coefficient -0.98.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902451&req=5

Figure 4: Relationship between Gauss-integrals distances and ARTS and LaJolla scores. (A) Average values of the ARTS scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 820,600 pairs of RNA chains. (B) Average values of the LaJolla TM scores (with standard deviations as vertical bars) as a function of Gauss-integrals distance. The calculations were carried out on the 5,050 pairs of tRNA chains. The dashed lines represent non-linear exponential curve fitting performed by GRACE program [30] with correlation coefficient -0.98.
Mentions: The Gauss-integrals based algorithm was benchmarked against the ARTS method by using all RNA structures that were suitable for ARTS, which does not process single chain molecules that lack base pairs. The correlation between the Gauss-integrals based distances and the ARTS similarity scores was analyzed. Figure 4A shows the relationship between the ARTS scores and the Gauss-integrals Euclidean distances. This relationship, determined on the basis of 820,600 pairs of RNA chains, can be fitted by the exponential curve

Bottom Line: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank.Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Structural and Computational Biology, Max F Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria. sviatlana.kirylava@univie.ac.at

ABSTRACT

Background: The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.

Results: The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.

Conclusions: The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

Show MeSH
Related in: MedlinePlus