Why Can't We Predict RNA Structure At Atomic Resolution?
Abstract
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.
Cite
@article{arxiv.1103.3032,
title = {Why Can't We Predict RNA Structure At Atomic Resolution?},
author = {Kyle Beauchamp and Parin Sripakdeevong and Rhiju Das},
journal= {arXiv preprint arXiv:1103.3032},
year = {2011}
}
Comments
K. Beauchamp & P. Sripakdeevong are equally contributing authors. Submission for book: RNA 3D Structure Analysis and Prediction, editors: N. Leontis & E. Westhof