{"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/explainablefold-understanding-alphafold","title":"ExplainableFold: Understanding AlphaFold Prediction with Explainable AI","arxiv_id":"2301.11765","date":"2023-01-27","proceeding":null,"authors":["Juntao Tan","Yongfeng Zhang"],"abstract":"This paper presents ExplainableFold, an explainable AI framework for protein structure prediction. Despite the success of AI-based methods such as AlphaFold in this field, the underlying reasons for their predictions remain unclear due to the black-box nature of deep learning models. To address this, we propose a counterfactual learning framework inspired by biological principles to generate counterfactual explanations for protein structure prediction, enabling a dry-lab experimentation approach. Our experimental results demonstrate the ability of ExplainableFold to generate high-quality explanations for AlphaFold's predictions, providing near-experimental understanding of the effects of amino acids on 3D protein structure. This framework has the potential to facilitate a deeper understanding of protein structures.","url_abs":"https://arxiv.org/abs/2301.11765v2","url_pdf":"https://arxiv.org/pdf/2301.11765v2.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":"explainablefold-understanding-alphafold","repo_url":"https://github.com/rutgerswiselab/ExplainableFold","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"prediction","task_name":"Prediction"},{"task_slug":"protein-structure-prediction","task_name":"Protein Structure Prediction"},{"task_slug":null,"task_name":"counterfactual"}],"methods":[{"method_slug":"alphafold","method_name":"AlphaFold"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2301.11765","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}