{"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/reactzyme-a-benchmark-for-enzyme-reaction","title":"ReactZyme: A Benchmark for Enzyme-Reaction Prediction","arxiv_id":"2408.13659","date":"2024-08-24","proceeding":null,"authors":["Chenqing Hua","Bozitao Zhong","Sitao Luan","Liang Hong","Guy Wolf","Doina Precup","Shuangjia Zheng"],"abstract":"Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation (https://github.com/WillHua127/ReactZyme).","url_abs":"https://arxiv.org/abs/2408.13659v3","url_pdf":"https://arxiv.org/pdf/2408.13659v3.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":"reactzyme-a-benchmark-for-enzyme-reaction","repo_url":"https://github.com/willhua127/reactzyme","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null},{"paper_slug":"reactzyme-a-benchmark-for-enzyme-reaction","repo_url":"https://github.com/willhua127/enzymeflow","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"NOASSERTION"}}],"tasks":[{"task_slug":"prediction","task_name":"Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2408.13659","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2408.13659"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/willhua127/reactzyme","reach":null},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/willhua127/enzymeflow","reach":{"status":"ok","spdx":"NOASSERTION"}}],"summary":{"ran_draft_wrong":3,"ran_honours":1},"by_repo_kind":{"official":{"samples":4,"ran":4,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"cf0c0ac0d19b0983","entry":"collate_fn","repo":"willhua127/reactzyme","repo_kind":"official","path":"data_utils.py","file_url":"https://github.com/willhua127/reactzyme/blob/HEAD/data_utils.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"CC0-1.0","inline_ok":true,"mcp_get_code":{"code_sha256":"cf0c0ac0d19b0983"}},{"code_sha256_prefix":"fc09fe92d0a51a4e","entry":"collate_fn_pretrained","repo":"willhua127/reactzyme","repo_kind":"official","path":"data_utils.py","file_url":"https://github.com/willhua127/reactzyme/blob/HEAD/data_utils.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"CC0-1.0","inline_ok":true,"mcp_get_code":{"code_sha256":"fc09fe92d0a51a4e"}},{"code_sha256_prefix":"9c4e721069783c6b","entry":"get_samples","repo":"willhua127/reactzyme","repo_kind":"official","path":"data_utils.py","file_url":"https://github.com/willhua127/reactzyme/blob/HEAD/data_utils.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"CC0-1.0","inline_ok":true,"mcp_get_code":{"code_sha256":"9c4e721069783c6b"}},{"code_sha256_prefix":"5a414eca5eaf8645","entry":"topk_accuracy","repo":"willhua127/reactzyme","repo_kind":"official","path":"retrieval.py","file_url":"https://github.com/willhua127/reactzyme/blob/HEAD/retrieval.py","link_basis":"first_harvest_node","language":"python","status":"ran_honours","verification_level":1,"contract_check":"HONOURS","metamorphic_tier":"invariant","behaviour_fingerprint":true,"licence":"CC0-1.0","inline_ok":true,"mcp_get_code":{"code_sha256":"5a414eca5eaf8645"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}