{"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/ranking-protein-protein-models-with-large","title":"Ranking protein-protein models with large language models and graph neural networks","arxiv_id":"2407.16375","date":"2024-07-23","proceeding":null,"authors":["Xiaotong Xu","Alexandre M. J. J. Bonvin"],"abstract":"Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere with those or to guide drug design. Various strategies can be followed to model those complexes, all typically resulting in a large number of models. A challenging step in this process is the identification of good models (near-native PPI conformations) from the large pool of generated models. To address this challenge, we previously developed DeepRank-GNN-esm, a graph-based deep learning algorithm for ranking modelled PPI structures harnessing the power of protein language models. Here, we detail the use of our software with examples. DeepRank-GNN-esm is freely available at https://github.com/haddocking/DeepRank-GNN-esm","url_abs":"https://arxiv.org/abs/2407.16375v1","url_pdf":"https://arxiv.org/pdf/2407.16375v1.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":"ranking-protein-protein-models-with-large","repo_url":"https://github.com/haddocking/deeprank-gnn-esm","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"drug-design","task_name":"Drug Design"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}