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RNA 3D-Modeling

Please always quote using this URN: urn:nbn:de:0297-zib-7708
  • This article presents a new computational approach to the three-dimensional (3D) modeling of ribonucleic acid (RNA) sequences with unknown spatial structure. The main concept is a mapping of the query sequence onto the 3D structures of a suitable template RNA molecule. This technique called \textit{threading} has originally been developed for the modeling of protein 3D structures. The application to RNA systems bridges the information gap between the growing mass of RNA sequence data and the relatively limited number of available 3D structures. The new RNA threading method is demonstrated on a tRNA model system because sufficient representative 3D structures have experimentally been elucidated and deposited in the public databases. Nevertheless, the method is in principle transferable on all other RNA species. Algorithms are developed that decompose these template structures into their secondary structure elements and gather this information in a specific template database. The best template is chosen with public alignment and secondary structure prediction tools which are integrated in the RNA modeling module. The structural information gathered from the template and the best alignment is combined to establish a comprehensive 3D model of the query sequence. A range of complete tRNA structures has successfully been modeled with the RNA threading method. The prototype module visualizes the models and provides convenient access to the proposed 3D structures. Therefore, the method could give new insight into a variety of RNA systems which in the recent years have become increasingly important as potential new pharmaceutical agents.

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Metadaten
Author:Alice Boit, Frank Cordes
Document Type:ZIB-Report
Tag:alignment; loop decomposition; relaxation; secondary structure; template library; threading
MSC-Classification:62-XX STATISTICS / 62Pxx Applications [See also 90-XX, 91-XX, 92-XX] / 62P10 Applications to biology and medical sciences
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C40 Biochemistry, molecular biology
Date of first Publication:2003/12/19
Series (Serial Number):ZIB-Report (03-48)
ZIB-Reportnumber:03-48
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