{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,14]],"date-time":"2026-11-14T04:32:35Z","timestamp":1794630755225,"version":"4.9.1"},"reference-count":48,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2027,2,1]],"date-time":"2027-02-01T00:00:00Z","timestamp":1801440000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100011933","name":"Chongqing Science and Technology Development Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011933","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2027,2]]},"DOI":"10.1016\/j.compbiolchem.2026.109368","type":"journal-article","created":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T23:16:47Z","timestamp":1788045407000},"page":"109368","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"P1","title":["GCAT-BCE: A hybrid GCN-GAT framework for enhanced conformational B-cell epitope prediction"],"prefix":"10.1016","volume":"126","author":[{"given":"Rui","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Lei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanxi","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Long","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5010-2978","authenticated-orcid":false,"given":"Hu","family":"Mei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2026.109368_bib1","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1146\/annurev-immunol-083122-044829","article-title":"B Cell-Directed Therapy in Autoimmunity","volume":"42","author":"Abeles","year":"2024","journal-title":"Annu. Rev. Immunol."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.109368_bib2","doi-asserted-by":"crossref","first-page":"2558","DOI":"10.1110\/ps.062405906","article-title":"Prediction of residues in discontinuous B-cell epitopes using protein 3D structures","volume":"15","author":"Andersen","year":"2006","journal-title":"Protein Sci."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109368_bib3","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109368_bib4","article-title":"B cell epitope prediction by capturing spatial clustering property of the epitopes using graph attention network","volume":"14","author":"Choi","year":"2024","journal-title":"Sci. Rep. -Uk"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib5","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2025.1646946","article-title":"BIDpred: unraveling B cell Immunodominance hierarchical pattern using statistical feature discovery and deep learning prediction","volume":"16","author":"Choi","year":"2025","journal-title":"Front. Immunol."},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.109368_bib6","doi-asserted-by":"crossref","DOI":"10.1002\/pro.4497","article-title":"BepiPred-3.0: Improved B-cell epitope prediction using protein language models","volume":"31","author":"Clifford","year":"2022","journal-title":"Protein Sci."},{"issue":"24","key":"10.1016\/j.compbiolchem.2026.109368_bib7","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adu1823","article-title":"AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding","volume":"11","author":"Clifford","year":"2025","journal-title":"Sci. Adv."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.109368_bib8","doi-asserted-by":"crossref","DOI":"10.1016\/j.jpha.2025.101316","article-title":"SITA: Predicting site-specific immunogenicity for therapeutic antibodies","volume":"15","author":"Cun","year":"2025","journal-title":"J. Pharm. Anal."},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109368_bib9","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab423","article-title":"epitope3D: a machine learning method for conformational B-cell epitope prediction","volume":"23","author":"Da Silva","year":"2022","journal-title":"Brief. Bioinform"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib10","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-017-1528-9","article-title":"SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence","volume":"18","author":"Dalkas","year":"2017","journal-title":"Bmc Bioinforma."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.109368_bib11","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01879-19","article-title":"Conformational Flexibility in Respiratory Syncytial Virus G Neutralizing Epitopes","volume":"94","author":"Fedechkin","year":"2020","journal-title":"J. Virol."},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.109368_bib12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0040104","article-title":"BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences","volume":"7","author":"Gao","year":"2012","journal-title":"Plos. One"},{"issue":"15","key":"10.1016\/j.compbiolchem.2026.109368_bib13","doi-asserted-by":"crossref","DOI":"10.3390\/ijms23158453","article-title":"CSatDTA: Prediction of Drug-Target Binding Affinity Using Convolution Model with Self-Attention","volume":"23","author":"Ghimire","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.compbiolchem.2026.109368_bib14","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2024.1322712","article-title":"DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations","volume":"15","author":"Hoie","year":"2024","journal-title":"Front. Immunol."},{"key":"10.1016\/j.compbiolchem.2026.109368_bib15","article-title":"Learning inverse folding from millions of predicted structures","author":"Hsu","year":"2022","journal-title":"J. ]. Pr. Mach. Learn. Res."},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109368_bib16","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbae084","article-title":"Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections","volume":"25","author":"Israeli","year":"2024","journal-title":"Brief. Bioinform"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109368_bib17","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbae084","article-title":"Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections","volume":"25","author":"Israeli","year":"2024","journal-title":"Brief. Bioinform"},{"issue":"W1","key":"10.1016\/j.compbiolchem.2026.109368_bib18","doi-asserted-by":"crossref","first-page":"W533","DOI":"10.1093\/nar\/gkae386","article-title":"SEMA 2.0: web-platform for B-cell conformational epitopes prediction using artificial intelligence","volume":"52","author":"Ivanisenko","year":"2024","journal-title":"Nucleic Acids Res."},{"issue":"W1","key":"10.1016\/j.compbiolchem.2026.109368_bib19","doi-asserted-by":"crossref","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"Jespersen","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2026.109368_bib20","article-title":"AlphaEpi: Enhancing B Cell Epitope Prediction with AlphaFold 3","volume":"2024","author":"Jiang","year":"2024"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib21","doi-asserted-by":"crossref","first-page":"D411","DOI":"10.1093\/nar\/gkq1105","article-title":"A series of PDB related databases for everyday needs","volume":"39","author":"Joosten","year":"2011","journal-title":"Nucleic Acids Res."},{"issue":"7873","key":"10.1016\/j.compbiolchem.2026.109368_bib22","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"issue":"12","key":"10.1016\/j.compbiolchem.2026.109368_bib23","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002829","article-title":"Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking","volume":"8","author":"Kringelum","year":"2012","journal-title":"Plos. Comput. Biol."},{"issue":"11","key":"10.1016\/j.compbiolchem.2026.109368_bib24","doi-asserted-by":"crossref","DOI":"10.1002\/pro.4785","article-title":"Multi-perspectives and challenges in identifying B-cell epitopes","volume":"32","author":"Kumar","year":"2023","journal-title":"Protein Sci."},{"key":"10.1016\/j.compbiolchem.2026.109368_bib25","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiomed.2024.108083","article-title":"A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence","volume":"170","author":"Kumar","year":"2024","journal-title":"Comput. Biol. Med."},{"issue":"10","key":"10.1016\/j.compbiolchem.2026.109368_bib26","doi-asserted-by":"crossref","DOI":"10.3390\/biom14101220","article-title":"PMSFF: Improved Protein Binding Residues Prediction through Multi-Scale Sequence-Based Feature Fusion Strategy","volume":"14","author":"Li","year":"2024","journal-title":"Biomolecules"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib27","doi-asserted-by":"crossref","DOI":"10.1002\/advs.202508896","article-title":"B-EPIC: A Transformer-Based Language Model for Decoding B Cell Immunodominance Patterns","author":"Liang","year":"2025","journal-title":"Adv. Sci."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.109368_bib28","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaf357","article-title":"Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics","volume":"26","author":"Lin","year":"2025","journal-title":"Brief. Bioinform"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib29","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-14-S2-S10","article-title":"Prediction of B-cell epitopes using evolutionary information and propensity scales","volume":"14","author":"Lin","year":"2013","journal-title":"Bmc Bioinforma."},{"issue":"6637","key":"10.1016\/j.compbiolchem.2026.109368_bib30","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib31","article-title":"A Structure-Based B-cell Epitope Prediction Model Through Combing Local and Global Features","volume":"13","author":"Lu","year":"2022","journal-title":"Front. Immunol."},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.109368_bib32","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbaf310","article-title":"Intelligent Batch Epitope Identification and Partitioning: an intelligent tool for the identification of B cell dominant epitopes","volume":"26","author":"Ma","year":"2025","journal-title":"Brief. Bioinform"},{"issue":"16","key":"10.1016\/j.compbiolchem.2026.109368_bib33","doi-asserted-by":"crossref","first-page":"2856","DOI":"10.1093\/bioinformatics\/bty1057","article-title":"MMseqs2 desktop and local web server app for fast, interactive sequence searches","volume":"35","author":"Mirdita","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib34","doi-asserted-by":"crossref","first-page":"189","DOI":"10.12688\/f1000research.7931.1","article-title":"FreeSASA: An open source C library for solvent accessible surface area calculations","volume":"5","author":"Mitternacht","year":"2016","journal-title":"F1000Research"},{"issue":"13","key":"10.1016\/j.compbiolchem.2026.109368_bib35","doi-asserted-by":"crossref","first-page":"3996","DOI":"10.1093\/bioinformatics\/btaa263","article-title":"Learning context-aware structural representations to predict antigen and antibody binding interfaces","volume":"36","author":"Pittala","year":"2020","journal-title":"Bioinformatics"},{"issue":"W1","key":"10.1016\/j.compbiolchem.2026.109368_bib36","doi-asserted-by":"crossref","first-page":"W59","DOI":"10.1093\/nar\/gku395","article-title":"SEPPA 2.0-more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen","volume":"42","author":"Qi","year":"2014","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"10.1016\/j.compbiolchem.2026.109368_bib37","doi-asserted-by":"crossref","DOI":"10.1002\/pro.70212","article-title":"HAIRpred: Prediction of human antibody interacting residues in an antigen from its primary structure","volume":"34","author":"Sahni","year":"2025","journal-title":"Protein Sci."},{"key":"10.1016\/j.compbiolchem.2026.109368_bib38","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.960985","article-title":"SEMA: Antigen B-cell conformational epitope prediction using deep transfer learning","volume":"13","author":"Shashkova","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.compbiolchem.2026.109368_bib39","doi-asserted-by":"crossref","unstructured":"Su J., Han C., Zhou Y., et al. SaProt: Protein Language Modeling with Structure-aware Vocabulary. 2024.","DOI":"10.1101\/2023.10.01.560349"},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.109368_bib40","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/s41592-022-01490-7","article-title":"ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction","volume":"19","author":"Tubiana","year":"2022","journal-title":"Nat. Methods"},{"issue":"2","key":"10.1016\/j.compbiolchem.2026.109368_bib41","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/0022-1759(86)90001-3","article-title":"Production and use of antibodies against synthetic peptides","volume":"88","author":"Walter","year":"1986","journal-title":"J. Immunol. Methods"},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.109368_bib42","article-title":"GraphEPN: A Deep Learning Framework for B-Cell Epitope Prediction Leveraging Graph Neural Networks","volume":"15","author":"Wang","year":"2025","journal-title":"Appl. Sci. -Basel"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib43","doi-asserted-by":"crossref","first-page":"2122","DOI":"10.1016\/j.csbj.2024.05.023","article-title":"WUREN: Whole-modal union representation for epitope prediction","volume":"23","author":"Wang","year":"2024","journal-title":"Comput. Struct. Biotec"},{"issue":"6","key":"10.1016\/j.compbiolchem.2026.109368_bib44","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbad345","article-title":"Spatom: a graph neural network for structure-based protein-protein interaction site prediction","volume":"24","author":"Wu","year":"2023","journal-title":"Brief. Bioinform"},{"issue":"1","key":"10.1016\/j.compbiolchem.2026.109368_bib45","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btag006","article-title":"RoBep: a region-oriented deep learning model for B-cell epitope prediction","volume":"42","author":"Xu","year":"2026","journal-title":"Bioinformatics"},{"issue":"4","key":"10.1016\/j.compbiolchem.2026.109368_bib46","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad187","article-title":"Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model","volume":"39","author":"Zeng","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2026.109368_bib47","article-title":"Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering","volume":"2014","author":"Zhang","year":"2014","journal-title":"Biomed. Res. Int."},{"issue":"W1","key":"10.1016\/j.compbiolchem.2026.109368_bib48","doi-asserted-by":"crossref","first-page":"W388","DOI":"10.1093\/nar\/gkz413","article-title":"SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens","volume":"47","author":"Zhou","year":"2019","journal-title":"Nucleic Acids Res."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126004950?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927126004950?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,11,14]],"date-time":"2026-11-14T04:13:58Z","timestamp":1794629638000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927126004950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2027,2]]},"references-count":48,"alternative-id":["S1476927126004950"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109368","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2027,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"GCAT-BCE: A hybrid GCN-GAT framework for enhanced conformational B-cell epitope prediction","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2026.109368","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"109368"}}