{"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/stapep-an-open-source-tool-for-the-structure","title":"StaPep: an open-source tool for the structure prediction and feature extraction of hydrocarbon-stapled peptides","arxiv_id":"2402.17997","date":"2024-02-28","proceeding":null,"authors":["Zhe Wang","Jianping Wu","Mengjun Zheng","Chenchen Geng","Borui Zhen","Wei zhang","Hui Wu","Zhengyang Xu","Gang Xu","Si Chen","Xiang Li"],"abstract":"Many tools exist for extracting structural and physiochemical descriptors from linear peptides to predict their properties, but similar tools for hydrocarbon-stapled peptides are lacking.Here, we present StaPep, a Python-based toolkit designed for generating 2D/3D structures and calculating 21 distinct features for hydrocarbon-stapled peptides.The current version supports hydrocarbon-stapled peptides containing 2 non-standard amino acids (norleucine and 2-aminoisobutyric acid) and 6 nonnatural anchoring residues (S3, S5, S8, R3, R5 and R8).Then we established a hand-curated dataset of 201 hydrocarbon-stapled peptides and 384 linear peptides with sequence information and experimental membrane permeability, to showcase StaPep's application in artificial intelligence projects.A machine learning-based predictor utilizing above calculated features was developed with AUC of 0.85, for identifying cell-penetrating hydrocarbon-stapled peptides.StaPep's pipeline spans data retrieval, cleaning, structure generation, molecular feature calculation, and machine learning model construction for hydrocarbon-stapled peptides.The source codes and dataset are freely available on Github: https://github.com/dahuilangda/stapep_package.","url_abs":"https://arxiv.org/abs/2402.17997v1","url_pdf":"https://arxiv.org/pdf/2402.17997v1.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":"stapep-an-open-source-tool-for-the-structure","repo_url":"https://github.com/dahuilangda/stapep_package","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"retrieval","task_name":"Retrieval"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}