Hamdani, H. Y., Appasamy, S. D., Willett, P. et al. (2 more authors) (2012) NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. Nucleic Acids Research, 40 (W1). W35. ISSN 0305-1048
Abstract
Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/.
Metadata
Item Type: | Article |
---|---|
Authors/Creators: |
|
Keywords: | Large ribosomal-subunit; Group-II Intron; Angstrom Resolution; 3D Structures; Base Triples; Database; Isomorphism; Patterns; Hairpin; Acids |
Dates: |
|
Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield) |
Depositing User: | Miss Anthea Tucker |
Date Deposited: | 09 Jan 2013 15:52 |
Last Modified: | 06 Jun 2014 22:42 |
Published Version: | http://dx.doi.org/10.1093/nar/gks513 |
Status: | Published |
Publisher: | Oxford University Press |
Identification Number: | 10.1093/nar/gks513 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:74879 |