{"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/building-confidence-in-deep-generative","title":"Building Confidence in Deep Generative Protein Design","arxiv_id":"2411.18568","date":"2024-11-27","proceeding":null,"authors":["Tianyuan Zheng","Alessandro Rondina","Pietro Liò"],"abstract":"Deep generative models show promise for de novo protein design, but their effectiveness within specific protein families remains underexplored. In this study, we evaluate two 3D rigid-body generative methods, score matching and flow matching, to generate monomeric protein backbones in SE(3) space. Our goal is to provide new insights and build confidence in the broader applicability of deep generative models for protein design. The optimal amino acid sequences were predicted from the generated backbones, followed by side-chain homology modeling. Results demonstrated high structural integrity, with conserved key residues aligning with known proteins. Structural phylogenetic analysis shows evolutionary links between the generated samples and their protein family members. Further molecular dynamics simulations and protein-ligand docking confirm the dynamic stability and functional potential of these samples, with ligand binding inducing conformational changes consistent with those in wild-type proteins.","url_abs":"https://arxiv.org/abs/2411.18568v1","url_pdf":"https://arxiv.org/pdf/2411.18568v1.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":"building-confidence-in-deep-generative","repo_url":"https://github.com/ecburx/proteval","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"protein-design","task_name":"Protein Design"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2411.18568","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2411.18568"}},"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/ecburx/proteval","reach":null}],"summary":{"unverified":5},"by_repo_kind":{"official":{"samples":5,"ran":0,"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":"74f24a368f6d26e6","entry":"descr","repo":"ecburx/proteval","repo_kind":"official","path":"notebooks/phylogeny/AFDB_tools.py","file_url":"https://github.com/ecburx/proteval/blob/HEAD/notebooks/phylogeny/AFDB_tools.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"74f24a368f6d26e6"}},{"code_sha256_prefix":"8abe09376cd5ef92","entry":"filter_plddt","repo":"ecburx/proteval","repo_kind":"official","path":"notebooks/phylogeny/AFDB_tools.py","file_url":"https://github.com/ecburx/proteval/blob/HEAD/notebooks/phylogeny/AFDB_tools.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"8abe09376cd5ef92"}},{"code_sha256_prefix":"f61dd45678f57f85","entry":"qscore","repo":"ecburx/proteval","repo_kind":"official","path":"src/phylogenetics.py","file_url":"https://github.com/ecburx/proteval/blob/HEAD/src/phylogenetics.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"f61dd45678f57f85"}},{"code_sha256_prefix":"6f1dcea4d1578ba0","entry":"rmsd_matrix","repo":"ecburx/proteval","repo_kind":"official","path":"src/phylogenetics.py","file_url":"https://github.com/ecburx/proteval/blob/HEAD/src/phylogenetics.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"6f1dcea4d1578ba0"}},{"code_sha256_prefix":"99252bdb43627c5a","entry":"tmalign","repo":"ecburx/proteval","repo_kind":"official","path":"src/phylogenetics.py","file_url":"https://github.com/ecburx/proteval/blob/HEAD/src/phylogenetics.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"99252bdb43627c5a"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}