ArticleNucleic acids research2012
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.Nucleic acids research · 2026Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp.Current microbiology · 2021Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- InterRNA: a database of base interactions in RNA structures.Nucleic acids research · 2016Article
- RAG-3D: a search tool for RNA 3D substructures.Nucleic acids research · 2015Article
- COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.Nucleic acids research · 2014Article
- Article
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5 authors.
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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/.
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