{"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/geometric-constraints-in-protein-folding","title":"Geometric constraints in protein folding","arxiv_id":"1812.09692","date":"2018-12-23","proceeding":null,"authors":[],"abstract":"The intricate three-dimensional geometries of protein tertiary structures\nunderlie protein function and emerge through a folding process from\none-dimensional chains of amino acids. The exact spatial sequence and\nconfiguration of amino acids, the biochemical environment and the temporal\nsequence of distinct interactions yield a complex folding process that cannot\nyet be easily tracked for all proteins. To gain qualitative insights into the\nfundamental mechanisms behind the folding dynamics and generic features of the\nfolded structure, we propose a simple model of structure formation that takes\ninto account only fundamental geometric constraints and otherwise assumes\nrandomly paired connections. We find that despite its simplicity, the model\nresults in a network ensemble consistent with key overall features of the\nensemble of Protein Residue Networks we obtained from more than 1000 biological\nprotein geometries as available through the Protein Data Base. Specifically,\nthe distribution of the number of interaction neighbors a unit (amino acid)\nhas, the scaling of the structure's spatial extent with chain length, the\neigenvalue spectrum and the scaling of the smallest relaxation time with chain\nlength are all consistent between model and real proteins. These results\nindicate that geometric constraints alone may already account for a number of\ngeneric features of protein tertiary structures.","url_abs":"http://arxiv.org/abs/1812.09692v1","url_pdf":"http://arxiv.org/pdf/1812.09692v1.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":"geometric-constraints-in-protein-folding","repo_url":"https://github.com/ppxasjsm/Geometric-constraints-protein-folding","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"protein-folding","task_name":"Protein Folding"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}