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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.

Show MeSH

Related in: MedlinePlus

The input form for FRASS server. It provides two possibilities to perform structural comparisons: on the one hand, the pair-wise comparison and, on the other, the database scan. The input files must be PDB-formatted. For database scanning, the cut-off distance and the number of similar structures can be specified (though reasonable default values are provided).
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Figure 1: The input form for FRASS server. It provides two possibilities to perform structural comparisons: on the one hand, the pair-wise comparison and, on the other, the database scan. The input files must be PDB-formatted. For database scanning, the cut-off distance and the number of similar structures can be specified (though reasonable default values are provided).

Mentions: The input form for the web server, referred to as FRASS, is shown in Figure 1. It requires the email address of the user and the (optional) title of the job. The user can perform the pair-wise comparison of two RNA structures or scan the database of RNA structures to find entries similar to the query. In the case of the pair-wise comparison, the two PDB files specified as "the query file" and "the second file" must be uploaded. If the PDB file contains more than one chain/model, the first chain/model will be considered. In the case of database scanning, only the query file must be uploaded. In this case the user can define two parameters: the Gauss-integrals distance cut-off and the number of the most similar structures which will be retained from the RNA database. The default values of these parameters are 0.5 and 10, respectively. Sample outputs of the FRASS server are shown in Figure 2 and Figure 3. The output of the pair-wise comparison includes the Gauss-integrals distance between the two structures (Figure 2). For example, the Gauss-integrals distance between two tRNA molecules with PDB identification codes 1J2B (chain C) and 1IL2 (chain C) is equal to 3.05. To estimate the statistical significance of this value, it was necessary to compute the distribution of the distances obtained for all pairs of RNA molecules of the database and in this case 90.70% of all the distances are larger than 3.05. This implies that only less than 10% of them are smaller and it suggests that this level of similarity is rather uncommon. The output of the database scanning is the list of the entries that are more similar than the cut-off distance. The RNA structure 1J2B (chain C) was chosen to exemplify the FRASS output (Figure 3). 1J2B is a tRNA with lambda-form that drastically differs from the typical tRNA L-shape. Whereas 141 tRNA structures are in one DARTS cluster, the chain C of 1J2B was registered as a false negative in the classification [18]. Most of the alignments of the C chain of 1J2B with other tRNA chains made with the LaJolla method result in a small number of pair-wise superpositions of equivalent nucleotides [17]. A multiple global structural alignment of the chain C of 1J2B with five tRNA chains (H4S_T, 1ASZ_R:620-660, 1IL2_C, 2CSX_C, 1EVV_A), created with the SARSA method, resulted in a large RMSD of 10.73 Å [15]. By using the chain C of 1J2B as a query in the FRASS database search mode (and by using a cut-off distance of 2.5 and by limiting to no more than 20 the number of database entries to be shown in the output), 15 tRNA chains were retained from the database (Figure 3). Their distances from the query are significantly small, since more than 92% of the possible distances are larger than them. This indicates, that the Gauss-integrals based method implemented into the FRASS server is able to successfully handle the difficult case of a tRNA chain (chain C of 1J2B) that is categorized into a cluster different from the cluster of other tRNAs in the DARTS classification.


FRASS: the web-server for RNA structural comparison.

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

The input form for FRASS server. It provides two possibilities to perform structural comparisons: on the one hand, the pair-wise comparison and, on the other, the database scan. The input files must be PDB-formatted. For database scanning, the cut-off distance and the number of similar structures can be specified (though reasonable default values are provided).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The input form for FRASS server. It provides two possibilities to perform structural comparisons: on the one hand, the pair-wise comparison and, on the other, the database scan. The input files must be PDB-formatted. For database scanning, the cut-off distance and the number of similar structures can be specified (though reasonable default values are provided).
Mentions: The input form for the web server, referred to as FRASS, is shown in Figure 1. It requires the email address of the user and the (optional) title of the job. The user can perform the pair-wise comparison of two RNA structures or scan the database of RNA structures to find entries similar to the query. In the case of the pair-wise comparison, the two PDB files specified as "the query file" and "the second file" must be uploaded. If the PDB file contains more than one chain/model, the first chain/model will be considered. In the case of database scanning, only the query file must be uploaded. In this case the user can define two parameters: the Gauss-integrals distance cut-off and the number of the most similar structures which will be retained from the RNA database. The default values of these parameters are 0.5 and 10, respectively. Sample outputs of the FRASS server are shown in Figure 2 and Figure 3. The output of the pair-wise comparison includes the Gauss-integrals distance between the two structures (Figure 2). For example, the Gauss-integrals distance between two tRNA molecules with PDB identification codes 1J2B (chain C) and 1IL2 (chain C) is equal to 3.05. To estimate the statistical significance of this value, it was necessary to compute the distribution of the distances obtained for all pairs of RNA molecules of the database and in this case 90.70% of all the distances are larger than 3.05. This implies that only less than 10% of them are smaller and it suggests that this level of similarity is rather uncommon. The output of the database scanning is the list of the entries that are more similar than the cut-off distance. The RNA structure 1J2B (chain C) was chosen to exemplify the FRASS output (Figure 3). 1J2B is a tRNA with lambda-form that drastically differs from the typical tRNA L-shape. Whereas 141 tRNA structures are in one DARTS cluster, the chain C of 1J2B was registered as a false negative in the classification [18]. Most of the alignments of the C chain of 1J2B with other tRNA chains made with the LaJolla method result in a small number of pair-wise superpositions of equivalent nucleotides [17]. A multiple global structural alignment of the chain C of 1J2B with five tRNA chains (H4S_T, 1ASZ_R:620-660, 1IL2_C, 2CSX_C, 1EVV_A), created with the SARSA method, resulted in a large RMSD of 10.73 Å [15]. By using the chain C of 1J2B as a query in the FRASS database search mode (and by using a cut-off distance of 2.5 and by limiting to no more than 20 the number of database entries to be shown in the output), 15 tRNA chains were retained from the database (Figure 3). Their distances from the query are significantly small, since more than 92% of the possible distances are larger than them. This indicates, that the Gauss-integrals based method implemented into the FRASS server is able to successfully handle the difficult case of a tRNA chain (chain C of 1J2B) that is categorized into a cluster different from the cluster of other tRNAs in the DARTS classification.

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