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Bioinformatics. 2013 Oct 15;29(20):2649-50. doi: 10.1093/bioinformatics/btt441. Epub 2013 Aug 7.

WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures.

Author information

1
Facultad de Ciencias Biologicas, Departamento de Genetica Molecular y Microbiologia, Pontificia Universidad Catolica de Chile, Alameda 340, Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Santiago, Chile and Division of Informatics, Department of Pathology, University of Alabama at Birmingham, 619 19 st. south, Birmingham, AL 35249, USA.

Abstract

SUMMARY:

The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and stability has become of great importance for characterizing their functional activity. Here, we introduce a new web application, WebRASP, that uses knowledge-based potentials for scoring RNA structures based on distance-dependent pairwise atomic interactions. This web server allows the users to upload a structure in PDB format, select several options to visualize the structure and calculate the energy profile. The server contains online help, tutorials and links to other related resources. We believe this server will be a useful tool for predicting and assessing the quality of RNA 3D structures.

AVAILABILITY AND IMPLEMENTATION:

The web server is available at http://melolab.org/webrasp. It has been tested on the most popular web browsers and requires Java plugin for Jmol visualization.

PMID:
23929030
PMCID:
PMC3789544
DOI:
10.1093/bioinformatics/btt441
[Indexed for MEDLINE]
Free PMC Article

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