Why Can't We Predict RNA Structure At Atomic Resolution? [chapter]

Parin Sripakdeevong, Kyle Beauchamp, Rhiju Das
2012 Nucleic acids and molecular biology  
No existing algorithm can start with arbitrary RNA sequences and return the precise three-dimensional structures that ensure their biological function. This chapter outlines current algorithms for automated RNA structure prediction (including our own FARNA-FARFAR), highlights their successes, and dissects their limitations, using a tetraloop and the sarcin/ricin motif as examples. The barriers to future advances are considered in light of three particular challenges: improving computational
more » ... ling, reducing reliance on experimentally solved structures, and avoiding coarse-grained representations of atomic-level interactions. To help meet these challenges and better understand the current state of the field, we propose an ongoing community-wide CASP-style experiment for evaluating the performance of current structure prediction algorithms. RNA as a Model System Predicting the three-dimensional structures of biopolymers from their primary sequence remains an unsolved but foundational problem in theoretical biophysics. This problem lies at the frontier of modern biological inquiry, encompassing questions from folding of individual protein and RNA domains to the fiber assembly of histone-compacted DNA genomes. However, a predictive, atomic-resolution
doi:10.1007/978-3-642-25740-7_4 fatcat:hcnwvqowmzbzpeo5rqotgmuiei