Why Can’t We Predict RNA Structure At Atomic Resolution?
- Parin SripakdeevongAffiliated withBiophysics Program, Stanford University
- , Kyle BeauchampAffiliated withBiophysics Program, Stanford University
- , Rhiju DasAffiliated withBiophysics Program, Stanford UniversityBiochemistry Department, Stanford University Email author
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 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.
- Why Can’t We Predict RNA Structure At Atomic Resolution?
- Book Title
- RNA 3D Structure Analysis and Prediction
- pp 43-65
- Print ISBN
- Online ISBN
- Series Title
- Nucleic Acids and Molecular Biology
- Series Volume
- Series ISSN
- Springer Berlin Heidelberg
- Copyright Holder
- Springer-Verlag Berlin Heidelberg
- Additional Links
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- Editor Affiliations
- ID1. Dept. Chemistry, Bowling Green State University
- ID2. Inst. Biologie Moleculaire, et Cellulaire, CNRS
- Author Affiliations
- 1. Biophysics Program, Stanford University, Stanford, CA, USA
- 2. Biochemistry Department, Stanford University, Stanford, CA, USA
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