RNA 3D-Modeling:
Abstract: "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...
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin
Konrad-Zuse-Zentrum für Informationstechnik
2003
|
| Schriftenreihe: | ZIB-Report
2003,48 |
| Schlagworte: | |
| Zusammenfassung: | Abstract: "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 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." |
| Beschreibung: | 30 S. Ill. |
Internformat
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| 490 | 1 | |a ZIB-Report |v 2003,48 | |
| 520 | 3 | |a Abstract: "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 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." | |
| 650 | 4 | |a Nucleotide sequence |x Computer simulation | |
| 650 | 4 | |a Three-dimensional imaging | |
| 700 | 1 | |a Cordes, Frank |e Verfasser |4 aut | |
| 830 | 0 | |a ZIB-Report |v 2003,48 |w (DE-604)BV013191727 |9 2003,48 | |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-012871438 | ||
Datensatz im Suchindex
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| any_adam_object | |
| author | Boit, Alice Cordes, Frank |
| author_facet | Boit, Alice Cordes, Frank |
| author_role | aut aut |
| author_sort | Boit, Alice |
| author_variant | a b ab f c fc |
| building | Verbundindex |
| bvnumber | BV019409423 |
| classification_rvk | SS 4779 |
| ctrlnum | (OCoLC)57072785 (DE-599)BVBBV019409423 |
| discipline | Informatik |
| format | Book |
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| id | DE-604.BV019409423 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:59:39Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-012871438 |
| oclc_num | 57072785 |
| open_access_boolean | |
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| owner_facet | DE-703 DE-188 |
| physical | 30 S. Ill. |
| publishDate | 2003 |
| publishDateSearch | 2003 |
| publishDateSort | 2003 |
| publisher | Konrad-Zuse-Zentrum für Informationstechnik |
| record_format | marc |
| series | ZIB-Report |
| series2 | ZIB-Report |
| spelling | Boit, Alice Verfasser aut RNA 3D-Modeling A. Boit ; F. Cordes Berlin Konrad-Zuse-Zentrum für Informationstechnik 2003 30 S. Ill. txt rdacontent n rdamedia nc rdacarrier ZIB-Report 2003,48 Abstract: "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 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." Nucleotide sequence Computer simulation Three-dimensional imaging Cordes, Frank Verfasser aut ZIB-Report 2003,48 (DE-604)BV013191727 2003,48 |
| spellingShingle | Boit, Alice Cordes, Frank RNA 3D-Modeling ZIB-Report Nucleotide sequence Computer simulation Three-dimensional imaging |
| title | RNA 3D-Modeling |
| title_auth | RNA 3D-Modeling |
| title_exact_search | RNA 3D-Modeling |
| title_full | RNA 3D-Modeling A. Boit ; F. Cordes |
| title_fullStr | RNA 3D-Modeling A. Boit ; F. Cordes |
| title_full_unstemmed | RNA 3D-Modeling A. Boit ; F. Cordes |
| title_short | RNA 3D-Modeling |
| title_sort | rna 3d modeling |
| topic | Nucleotide sequence Computer simulation Three-dimensional imaging |
| topic_facet | Nucleotide sequence Computer simulation Three-dimensional imaging |
| volume_link | (DE-604)BV013191727 |
| work_keys_str_mv | AT boitalice rna3dmodeling AT cordesfrank rna3dmodeling |