{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/elastic-network-models-for-rna-a-comparative","title":"Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments","arxiv_id":"1506.09178","date":"2015-06-30","proceeding":null,"authors":[],"abstract":"Elastic network models (ENMs) are valuable and efficient tools for\ncharacterizing the collective internal dynamics of proteins based on the\nknowledge of their native structures. The increasing evidence that the\nbiological functionality of RNAs is often linked to their innate internal\nmotions, poses the question of whether ENM approaches can be successfully\nextended to this class of biomolecules. This issue is tackled here by\nconsidering various families of elastic networks of increasing complexity\napplied to a representative set of RNAs. The fluctuations predicted by the\nalternative ENMs are stringently validated by comparison against extensive\nmolecular dynamics simulations and SHAPE experiments. We find that simulations\nand experimental data are systematically best reproduced by either an all-atom\nor a three-beads-per-nucleotide representation (sugar-base-phosphate), with the\nlatter arguably providing the best balance of accuracy and computational\ncomplexity.","url_abs":"http://arxiv.org/abs/1506.09178v1","url_pdf":"http://arxiv.org/pdf/1506.09178v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"elastic-network-models-for-rna-a-comparative","repo_url":"https://github.com/srnas/barnaba","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}