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

Details Why Can't We Predict RNA Structure At Atomic Resolution? Why Can't We Predict RNA Structure At Atomic Resolution?

2011-03-15

arxiv.org/abs/1103.3032v1

Biology

Quantitative Biology

Biomolecules

K. Beauchamp & P. Sripakdeevong are equally contributing authors. Submission for book: RNA 3D Structure Analysis and Predictio

Scientific paper

No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures 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 sampling, 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.

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