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Biophys J. 2017 Jul 25;113(2):225-234. doi: 10.1016/j.bpj.2016.12.037. Epub 2017 Feb 2.

Opportunities and Challenges in RNA Structural Modeling and Design.

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Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York. Electronic address:
Department of Molecular and Cellular and Developmental Biology and Department of Chemistry, Yale University; Howard Hughes Medical Institute, New Haven, Connecticut. Electronic address:


We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures. We discuss various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design, and the complementary roles that both atomistic and coarse-grained approaches play in such simulations. Collectively, as scientists from varied disciplines become familiar and drawn into these unique challenges, new approaches and collaborative efforts will undoubtedly be catalyzed.

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