دورية أكاديمية
Network Properties of the Ensemble of RNA Structures.
| العنوان: | Network Properties of the Ensemble of RNA Structures. |
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| المؤلفون: | Peter Clote, Amir Bayegan |
| المصدر: | PLoS ONE, Vol 10, Iss 10, p e0139476 (2015) |
| بيانات النشر: | Public Library of Science (PLoS), 2015. |
| سنة النشر: | 2015 |
| المجموعة: | LCC:Medicine LCC:Science |
| مصطلحات موضوعية: | Medicine, Science |
| الوصف: | We describe the first dynamic programming algorithm that computes the expected degree for the network, or graph G = (V, E) of all secondary structures of a given RNA sequence a = a1, …, an. Here, the nodes V correspond to all secondary structures of a, while an edge exists between nodes s, t if the secondary structure t can be obtained from s by adding, removing or shifting a base pair. Since secondary structure kinetics programs implement the Gillespie algorithm, which simulates a random walk on the network of secondary structures, the expected network degree may provide a better understanding of kinetics of RNA folding when allowing defect diffusion, helix zippering, and related conformation transformations. We determine the correlation between expected network degree, contact order, conformational entropy, and expected number of native contacts for a benchmarking dataset of RNAs. Source code is available at http://bioinformatics.bc.edu/clotelab/RNAexpNumNbors. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1932-6203 |
| Relation: | http://europepmc.org/articles/PMC4619022?pdf=render; https://doaj.org/toc/1932-6203 |
| DOI: | 10.1371/journal.pone.0139476 |
| URL الوصول: | https://doaj.org/article/d6e975d1eaff41d8b8017d0474940d3c |
| رقم الأكسشن: | edsdoj.6e975d1eaff41d8b8017d0474940d3c |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 19326203 |
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| DOI: | 10.1371/journal.pone.0139476 |