{"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/predicting-mutational-effects-on-protein-1","title":"Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model","arxiv_id":"2310.19849","date":"2023-10-30","proceeding":"NeurIPS 2023 11","authors":["Shiwei Liu","Tian Zhu","Milong Ren","Chungong Yu","Dongbo Bu","Haicang Zhang"],"abstract":"Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is vital in protein engineering and therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on generating protein backbone structures.","url_abs":"https://arxiv.org/abs/2310.19849v1","url_pdf":"https://arxiv.org/pdf/2310.19849v1.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":"predicting-mutational-effects-on-protein-1","repo_url":"https://github.com/eurekazhu/diffaffinity","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"jax","reach":null}],"tasks":[{"task_slug":"representation-learning","task_name":"Representation Learning"}],"methods":[{"method_slug":"diffusion","method_name":"Diffusion"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}