{"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/cbgbench-fill-in-the-blank-of-protein","title":"CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph","arxiv_id":"2406.10840","date":"2024-06-16","proceeding":null,"authors":["Haitao Lin","Guojiang Zhao","Odin Zhang","Yufei Huang","Lirong Wu","Zicheng Liu","Siyuan Li","Cheng Tan","Zhifeng Gao","Stan Z. Li"],"abstract":"Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative heterogeneous graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements various cutting-edge methods. Secondly, a single task on \\textit{de novo} molecule generation can hardly reflect their capabilities. To broaden the scope, we have adapted these models to a range of tasks essential in drug design, which are considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of \\textit{de novo} molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide the pre-trained versions of the state-of-the-art models and deep insights with analysis from empirical studies. The codebase for CBGBench is publicly accessible at \\url{https://github.com/Edapinenut/CBGBench}.","url_abs":"https://arxiv.org/abs/2406.10840v3","url_pdf":"https://arxiv.org/pdf/2406.10840v3.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":"cbgbench-fill-in-the-blank-of-protein","repo_url":"https://github.com/edapinenut/cbgbench","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"drug-design","task_name":"Drug Design"},{"task_slug":"fairness","task_name":"Fairness"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2406.10840","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2406.10840"}},"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/edapinenut/cbgbench","reach":null}],"summary":{"ran_draft_wrong":1},"by_repo_kind":{},"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":1,"samples":[{"code_sha256_prefix":"9e1530a4c6d98ce0","entry":"get_all_deepest_subfolders","repo":null,"repo_kind":null,"path":null,"file_url":null,"link_basis":"identical_code_first_harvested_elsewhere","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":true,"licence":null,"inline_ok":false,"mcp_get_code":{"code_sha256":"9e1530a4c6d98ce0"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}