{"doi":"10.1021/acs.jcim.5c03075","title":"Physical Implausibility of Carbohydrate Ligands in Results of Deep Learning-Based Cofolding Methods","abstract":null,"journal":"Journal of Chemical Information and Modeling","year":2026,"id":613388,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":827811,"name":"Adam J. Simpkin","orcid":"0000-0003-1883-9376","position":1,"is_corresponding":false},{"id":1580221,"name":"Luc G. Elliott","orcid":null,"position":2,"is_corresponding":false},{"id":1222635,"name":"Pornthep Sompornpisut","orcid":"0000-0002-8029-332X","position":3,"is_corresponding":false},{"id":555893,"name":"Daniel J. Rigden","orcid":"0000-0002-7565-8937","position":4,"is_corresponding":false},{"id":1580220,"name":"Muhammad Luthfi","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Physical Implausibility of Carbohydrate Ligands in Results of Deep Learning-Based Cofolding Methods","abstract":"High Resolution Image Download MS PowerPoint Slide Stereochemistry violations in AlphaFold 3 models are more prevalent than currently appreciated. Analysis of 900 carbohydrate ligands revealed that 85.8% have errors, mainly in chirality but also including bond conversions (15.2%), planar ring distortions (3.9%), aromatic ring formations (2.5%), and improper structural configurations (0.9%). Boltz-1x reduced most violations dramatically but increased improper configurations to 22.1%, notably in N -acetyl-α-neuraminic acid. The BondedAtomPairs protocol reduced stereochemical issues but lost the reducing-end anomeric oxygen, highlighting ongoing challenges in accurate carbohydrate modeling.","is_dataset_classified":null,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"41866819","pmcid":"PMC13080964","openalex_id":"https://openalex.org/W7140083329","authors":[],"funders":[{"funder_name":"Chulalongkorn University","grant_id":"","title":null}],"total_grants":1,"fwci":3.5115,"citation_percentile":0.91873774,"influential_citations":0,"citation_trend":[{"year":2026,"count":1}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c03075?ref=article_openPDF","host_type":"journal"},{"url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c03075?ref=article_openPDF","host_type":"publisher"},{"url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c03075","host_type":"publisher"},{"url":"https://doi.org/10.1021/acs.jcim.5c03075","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/41866819","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13080964/","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC13080964","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC13080964?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Molecular spectroscopy and chirality","Protein Structure and Dynamics","Enzyme Structure and Function"],"mesh_terms":["Deep Learning","Carbohydrate Conformation","Carbohydrates","Ligands","Models, Molecular","Stereoisomerism"],"keywords":["Carbohydrate","Ring (chemistry)","Anomer","Chirality (physics)","Carbohydrate chemistry","Carbohydrate conformation","Molecular conformation"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T07:55:47.491719Z","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":[]}