Physics-based RNA structure prediction
نویسندگان
چکیده
منابع مشابه
Physics-based RNA structure prediction
Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a numbe...
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MOTIVATION For several decades, free energy minimization methods have been the dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars (SCFGs) have emerged as an alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally-measured thermodynamic paramete...
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Various systems have been proposed to predict secondary structures of RNAs using their sequence information. Among them, Uemura et al. [2] described a system that recognizes some typical RNA secondary structures such as hairpin loops and pseudoknots with Tree Adjoining Grammar. However, their work captures only known sub-structures, and not those unknown sub-structures that might also exist. Te...
متن کاملPhysics-based de novo prediction of RNA 3D structures.
Current experiments on structural determination cannot keep up the pace with the steadily emerging RNA sequences and new functions. This underscores the request for an accurate model for RNA three-dimensional (3D) structural prediction. Although considerable progress has been made in mechanistic studies, accurate prediction for RNA tertiary folding from sequence remains an unsolved problem. The...
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The view of RNA as simple information transfer molecule has been continuously challenged since the discovery of ribozymes, a class of RNA molecules with enzyme-like function. Moreover, the recent discovery of tiny RNA molecules such as RNAs and small interfering RNA, is transforming our thinking about how gene expression is regulated. Thus, RNA molecules are now known to carry a large repertory...
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ژورنال
عنوان ژورنال: Biophysics Reports
سال: 2015
ISSN: 2364-3439,2364-3420
DOI: 10.1007/s41048-015-0001-4