{"doi":"10.1145/3580305.3599337","title":"ExplainableFold: Understanding AlphaFold Prediction with Explainable AI","abstract":"This paper presents ExplainableFold (xFold), which is an Explainable AI framework for protein structure prediction. Despite the success of AI-based methods such as AlphaFold (αFold) 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. Source code and data of the ExplainableFold project are available at https://github.com/rutgerswiselab/ExplainableFold.","journal":null,"year":2023,"id":390011,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9545,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1161244,"name":"Yongfeng Zhang","orcid":"0000-0003-2633-8555","position":1,"is_corresponding":false},{"id":1161243,"name":"Juntao Tan","orcid":"0000-0003-3646-933X","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":null,"created_at":"2026-07-19T01:18:32.854511Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}