RRM
2008 Rustbelt RNA Meeting
RRM
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Poster abstracts
Abstract:
Find RNA 3D (FR3D), is a suite of programs for finding motifs in RNA atomic-resolution 3D structures. A base-centered approach was implemented to construct efficient, yet exhaustive motif search procedures using geometric, symbolic, or mixed representations of RNA structure. For geometric searches, a user-supplied 3D Query Motif is used to find and score geometrically similar candidate motifs, without regard to nucleotide identity or the sequential position of their nucleotides in the RNA chain or chains. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by first rigidly rotating candidate motifs to optimally align with the Query Motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Candidate motifs may be screened using symbolic constraints to identify those that contain particular bases, basepair types, base-stacking arrangements, base-phosphate interactions, or that conform to sequence continuity constraints. Purely symbolic searches for motifs are also implemented. The Display module provides tools to view, align, cluster and calculate an exemplar for the candidate motifs. It also allows one to superimpose motifs and display neighborhoods. Searches can be saved and written out to PDB files. FR3D is an open source software that has been developed and tested under Windows XP/Mac OS X 10.4, and is capable of running on any PC or Mac platform with Matlab 7.4 or higher installed version. A stand-alone version is also available for the PC platform. FR3D can be downloaded at: http://rna.bgsu.edu/FR3D.
Keywords: RNA 3D Motif, Geometric Search, Interactions
