3D pattern searching in nucleic acid structures
The NASSAM program searches for motifs and formations of nucleic acid bases in 3D space within nucleic acid (and nucleic acid associated) PDB formatted structures. The searches are based on distances between the bases which are represented as pseudoatom vectors. This search is independent of the base sequence order.

Primary References:
1. Hazrina Y. Hamdani, Sri D. Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. Nucleic Acids Research. doi: 10.1093/nar/gks513. HTML, PDF
2. Firdaus-Raih, M., Harrison, A-M, Willett, P., and Artymiuk, P.J. (2011) Novel base triples in RNA structures revealed by graph theoretical searching methods. BMC Bioinformatics, 12(S13): S2.
3. Harrison, A-M., South, D.R., Willett, P., and Artymiuk, P.J. (2003) Representation, searching and discovery of patterns of bases in complex RNA structures. Journal of Computer-Aided Molecular Design, 17, 537-549.

Guide to submitting a search:
1. Please ensure that the query structure is a PDB formatted file. (See test/demo submission)
2. The program typically takes 2-5 minutes to complete depending on the size of your nucleic acid structure. Thank you for your patience.
3. The distance tolerance has been set to an optimized value as the default.
   - To increase retrieval or coverage of the search, increase the distance tolerance value.
   (Note: This may also result in an increase of false positive results)

[see NASSAM Help pages]

Search RNA Structure for: (in PDB format/CIF format)

Demonstration run:

This is a demonstration NASSAM run searching for base triples in the structure 3q1r.pdb, the structure of a bacterial ribonuclease P holoenzyme in complex with tRNA.

Precomputed example:
Click here to view the precomputed results of a NASSAM search using 3Q1R.pdb as input.

Click here to view the precomputed results of a NASSAM search for tloop motifs using 1FFK.pdb as input.

Click here to view the precomputed results of a NASSAM search for tetraloops using 1FFK.pdb as input.

Please contact info_at_mfrlab.org ( _at_ = @ ) for any queries or to report errors.