title: ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments.
abstract: The existence and identity of non-Watson-Crick base pairs (bps) within RNA bulges, internal loops, and hairpin loops cannot reliably be predicted by existing algorithms. We have developed the Isfold (Isosteric Folding) program as a tool to examine patterns of nucleotide substitutions from sequence alignments or mutation experiments and identify plausible bp interactions. We infer these interactions based on the observation that each non-Watson-Crick bp has a signature pattern of isosteric substitutions where mutations can be made that preserve the 3D structure. Isfold produces a dynamic representation of predicted bps within defined motifs in order of their probabilities. The software was developed under Windows XP, and is capable of running on PC and MAC with Matlab 7.1 (SP3) or higher. A PC stand-alone version that does not require Matlab also is available. This software and a user manual are freely available at www.ucsf.edu/frankel/isfold.
authors.affiliation: Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, CA 94143-2280, USA. Ali.Mokdad@ucsf.edu
authors.forename: Ali
authors.initials: A
authors.lastname: Mokdad
authors.forename: Alan D
authors.initials: AD
authors.lastname: Frankel
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012313:RNA