NASSAM: A server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules

Hazrina Y. Hamdani, Sri D. Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus Mohd Raih

Research output: Contribution to journalArticle

11 Citations (Scopus)

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/.

Original languageEnglish
JournalNucleic Acids Research
Volume40
Issue numberW1
DOIs
Publication statusPublished - Jul 2012

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Nucleic Acids
RNA

ASJC Scopus subject areas

  • Genetics

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NASSAM : A server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. / Hamdani, Hazrina Y.; Appasamy, Sri D.; Willett, Peter; Artymiuk, Peter J.; Mohd Raih, Mohd Firdaus.

In: Nucleic Acids Research, Vol. 40, No. W1, 07.2012.

Research output: Contribution to journalArticle

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