{"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/egr-equivariant-graph-refinement-and","title":"EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures","arxiv_id":"2205.10390","date":"2022-05-20","proceeding":null,"authors":["Alex Morehead","Xiao Chen","Tianqi Wu","Jian Liu","Jianlin Cheng"],"abstract":"Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a notable influence on the biological function of the complex, computational methods that can quickly and effectively be used to refine and assess the quality of a protein complex's 3D structure can directly be used within a drug discovery pipeline to accelerate the development of new therapeutics and improve the efficacy of future vaccines. In this work, we introduce the Equivariant Graph Refiner (EGR), a novel E(3)-equivariant graph neural network (GNN) for multi-task structure refinement and assessment of protein complexes. Our experiments on new, diverse protein complex datasets, all of which we make publicly available in this work, demonstrate the state-of-the-art effectiveness of EGR for atomistic refinement and assessment of protein complexes and outline directions for future work in the field. In doing so, we establish a baseline for future studies in macromolecular refinement and structure analysis.","url_abs":"https://arxiv.org/abs/2205.10390v2","url_pdf":"https://arxiv.org/pdf/2205.10390v2.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":"egr-equivariant-graph-refinement-and","repo_url":"https://github.com/BioinfoMachineLearning/DeepRefine","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"GPL-3.0"}}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":"graph-neural-network","task_name":"Graph Neural Network"}],"methods":[{"method_slug":"graph-neural-network","method_name":"Graph Neural Network"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2205.10390","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}