Identifying novel sequence variants of RNA 3D motifs

Predicting RNA 3D structure from sequence is a ma-jor challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochas-tic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are con-structed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions gen-erated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas han-dle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Vali-dation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to auto-matically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download