{"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/highly-accurate-and-efficient-deep-learning","title":"Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop","arxiv_id":"2306.12754","date":"2023-06-22","proceeding":null,"authors":["Tianyue Wang","Xujun Zhang","Odin Zhang","Peichen Pan","Guangyong Chen","Yu Kang","Chang-Yu Hsieh","Tingjun Hou"],"abstract":"Protein loop modeling is the most challenging yet highly non-trivial task in protein structure prediction. Despite recent progress, existing methods including knowledge-based, ab initio, hybrid and deep learning (DL) methods fall significantly short of either atomic accuracy or computational efficiency. Moreover, an overarching focus on backbone atoms has resulted in a dearth of attention given to side-chain conformation, a critical aspect in a host of downstream applications including ligand docking, molecular dynamics simulation and drug design. To overcome these limitations, we present KarmaLoop, a novel paradigm that distinguishes itself as the first DL method centered on full-atom (encompassing both backbone and side-chain heavy atoms) protein loop modeling. Our results demonstrate that KarmaLoop considerably outperforms conventional and DL-based methods of loop modeling in terms of both accuracy and efficiency, with the average RMSD improved by over two-fold compared to the second-best baseline method across different tasks, and manifests at least two orders of magnitude speedup in general. Consequently, our comprehensive evaluations indicate that KarmaLoop provides a state-of-the-art DL solution for protein loop modeling, with the potential to hasten the advancement of protein engineering, antibody-antigen recognition, and drug design.","url_abs":"https://arxiv.org/abs/2306.12754v1","url_pdf":"https://arxiv.org/pdf/2306.12754v1.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":"highly-accurate-and-efficient-deep-learning","repo_url":"https://github.com/karma211225/karmaloop","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"computational-efficiency","task_name":"Computational Efficiency"},{"task_slug":"drug-design","task_name":"Drug Design"},{"task_slug":"protein-structure-prediction","task_name":"Protein Structure Prediction"}],"methods":[{"method_slug":"focus","method_name":"Focus"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}