{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T12:19:44Z","timestamp":1763468384381,"version":"3.37.3"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,9,18]],"date-time":"2017-09-18T00:00:00Z","timestamp":1505692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100011512","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011512","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007431","name":"NRF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The identification of T-cell epitopes has many profound translational applications in the areas of transplantation, disease diagnosis, vaccine\/therapeutic protein development and personalized immunotherapy. While data-driven methods have been widely used for the prediction of peptide binders with notable successes, the structural modeling of peptide binding to MHC molecules is crucial for understanding the underlying molecular mechanism of the immunological processes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed GradDock, a structure-based method for the rapid and accurate modeling of peptide binding to MHC Class I (pMHC-I). GradDock explicitly models diverse unbound peptides in vacuo and inserts them into the MHC-I groove through a steered gradient descent with a topological correction process. The simulation process yields diverse structural conformations including native-like peptides. We completely revised the Rosetta score terms and developed a new ranking function specifically for pMHC-I. Using the diverse peptides, a linear programming approach is applied to find the optimal weights for the individual Rosetta score terms. Our examination revealed that a refinement of the dihedral angles and a modification of the repulsion can dramatically improve the modeling quality. GradDock is five-times faster than a Rosetta-based docking approach for pMHC-I. We also demonstrate that the predictive capability of GradDock with the re-weighted Rosetta ranking function is consistently more accurate than the Rosetta-based method with the standard Rosetta score (approximately three-times better for a cross-docking set).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GradDock is freely available for academic purposes. The program and the ranking score weights for Rosetta are available at http:\/\/bel.kaist.ac.kr\/research\/GradDock.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx589","type":"journal-article","created":{"date-parts":[[2017,9,15]],"date-time":"2017-09-15T11:08:59Z","timestamp":1505473739000},"page":"469-476","source":"Crossref","is-referenced-by-count":26,"title":["GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking"],"prefix":"10.1093","volume":"34","author":[{"given":"Hyun-Ho","family":"Kyeong","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea"}]},{"given":"Yoonjoo","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea"}]},{"given":"Hak-Sung","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea"}]}],"member":"286","published-online":{"date-parts":[[2017,9,18]]},"reference":[{"key":"2023012712320334100_btx589-B1","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1034\/j.1399-0039.2000.550603.x","article-title":"Poor correspondence between predicted and experimental binding of peptides to class I MHC molecules","volume":"55","author":"Andersen","year":"2000","journal-title":"Tissue Antigens"},{"key":"2023012712320334100_btx589-B2","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/bioinformatics\/btv639","article-title":"Gapped sequence alignment using artificial neural networks: application to the MHC class I system","volume":"32","author":"Andreatta","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012712320334100_btx589-B3","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1002\/prot.22629","article-title":"DynaDock: A new molecular dynamics-based algorithm for protein\u2013peptide docking including receptor flexibility","volume":"78","author":"Antes","year":"2010","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712320334100_btx589-B4","doi-asserted-by":"crossref","first-page":"e41710.","DOI":"10.1371\/journal.pone.0041710","article-title":"Predicting HLA class I non-permissive amino acid residues substitutions","volume":"7","author":"Binkowski","year":"2012","journal-title":"PLoS One"},{"key":"2023012712320334100_btx589-B5","doi-asserted-by":"crossref","first-page":"15021.","DOI":"10.1038\/mtm.2015.21","article-title":"Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance","volume":"2","author":"Blazanovic","year":"2015","journal-title":"Mol. Therapy Methods Clin. Dev"},{"key":"2023012712320334100_btx589-B6","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1002\/prot.20831","article-title":"Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes","volume":"63","author":"Bordner","year":"2006","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712320334100_btx589-B7","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1126\/science.8023162","article-title":"Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules","volume":"265","author":"Bouvier","year":"1994","journal-title":"Science"},{"key":"2023012712320334100_btx589-B8","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1002\/prot.20870","article-title":"Structural prediction of peptides binding to MHC class I molecules","volume":"63","author":"Bui","year":"2006","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712320334100_btx589-B9","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1110\/ps.0242703","article-title":"Cyclic coordinate descent: a robotics algorithm for protein loop closure","volume":"12","author":"Canutescu","year":"2003","journal-title":"Protein Sci"},{"key":"2023012712320334100_btx589-B10","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.7717\/peerj.1","article-title":"How long is a piece of loop?","volume":"1","author":"Choi","year":"2013","journal-title":"PeerJ"},{"key":"2023012712320334100_btx589-B11","first-page":"1045","volume-title":"MAbs","author":"Choi","year":"2015"},{"key":"2023012712320334100_btx589-B12","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.jmb.2005.11.059","article-title":"Structural prediction of peptides bound to MHC class I","volume":"356","author":"Fagerberg","year":"2006","journal-title":"J. Mol. Biol"},{"key":"2023012712320334100_btx589-B13","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1007\/BF02093474","article-title":"Measurements of the relative permittivity of liquid water at frequencies in the range of 0.1 to 10\u2009kHz and at temperatures between 273.1 and 373.2 K at ambient pressure","volume":"16","author":"Fern\u00e1ndez","year":"1995","journal-title":"Int. J. Thermophys"},{"key":"2023012712320334100_btx589-B14","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/nm1461","article-title":"Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants","volume":"13","author":"Fischer","year":"2007","journal-title":"Nat. Med"},{"key":"2023012712320334100_btx589-B15","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1007\/s00726-010-0579-2","article-title":"Evaluation of different generic in silico methods for predicting HLA class I binding peptide vaccine candidates using a reverse approach","volume":"39","author":"Gowthaman","year":"2010","journal-title":"Amino Acids"},{"key":"2023012712320334100_btx589-B16","doi-asserted-by":"crossref","first-page":"D208","DOI":"10.1093\/nar\/gkh042","article-title":"IMGT\/3Dstructure-DB and IMGT\/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data","volume":"32","author":"Kaas","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023012712320334100_btx589-B17","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1745-7580-6-S1-S2","article-title":"pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes","volume":"6","author":"Khan","year":"2010","journal-title":"Immunome Res"},{"key":"2023012712320334100_btx589-B18","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1073\/pnas.1321126111","article-title":"Removing T-cell epitopes with computational protein design","volume":"111","author":"King","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712320334100_btx589-B19","first-page":"bbv005","article-title":"Current status and future challenges in T-cell receptor\/peptide\/MHC molecular dynamics simulations","author":"Knapp","year":"2015","journal-title":"Brief. Bioinf"},{"key":"2023012712320334100_btx589-B20","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1097\/QCO.0b013e32813e3fd8","article-title":"T cell-based diagnosis of childhood tuberculosis infection","volume":"20","author":"Lalvani","year":"2007","journal-title":"Curr. Opin. Infect. Dis"},{"key":"2023012712320334100_btx589-B21","doi-asserted-by":"crossref","first-page":"1986","DOI":"10.1016\/j.molimm.2006.09.029","article-title":"A molecular immunology approach to antibody humanization and functional optimization","volume":"44","author":"Lazar","year":"2007","journal-title":"Mol. Immunol"},{"key":"2023012712320334100_btx589-B22","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1016\/j.dci.2005.03.003","article-title":"IMGT unique numbering for MHC groove G-domain and MHC superfamily (MhcSF) G-like-domain","volume":"29","author":"Lefranc","year":"2005","journal-title":"Dev. Compar. Immunol"},{"key":"2023012712320334100_btx589-B23","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1016\/S0140-6736(04)17592-2","article-title":"Diagnosis of tuberculosis in South African children with a T cell-based assay: a prospective cohort study","volume":"364","author":"Liebeschuetz","year":"2004","journal-title":"Lancet"},{"key":"2023012712320334100_btx589-B24","doi-asserted-by":"crossref","first-page":"S3.","DOI":"10.1186\/1745-7580-6-S2-S3","article-title":"State of the art and challenges in sequence based T-cell epitope prediction","volume":"6","author":"Lundegaard","year":"2010","journal-title":"Immunome Res"},{"key":"2023012712320334100_btx589-B25","doi-asserted-by":"crossref","first-page":"W509","DOI":"10.1093\/nar\/gkn202","article-title":"NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8\u201311","volume":"36","author":"Lundegaard","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023012712320334100_btx589-B26","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1016\/0022-2836(92)90228-C","article-title":"Contact potential that recognizes the correct folding of globular proteins","volume":"227","author":"Maiorov","year":"1992","journal-title":"J. Mol. Biol"},{"key":"2023012712320334100_btx589-B27","first-page":"mdv382","article-title":"Targeting the undruggable: immunotherapy meets personalized oncology in the genomic era","author":"Martin","year":"2015","journal-title":"Ann. Oncol"},{"key":"2023012712320334100_btx589-B28","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1126\/science.1323878","article-title":"Emerging principles for the recognition of peptide antigens by MHC class I molecules","volume":"257","author":"Matsumura","year":"1992","journal-title":"Science"},{"key":"2023012712320334100_btx589-B29","doi-asserted-by":"crossref","first-page":"8571","DOI":"10.1073\/pnas.1405153111","article-title":"Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes","volume":"111","author":"Mazor","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712320334100_btx589-B30","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.jim.2015.06.003","article-title":"Poor correlation between T-cell activation assays and HLA-DR binding prediction algorithms in an immunogenic fragment of Pseudomonas exotoxin A","volume":"425","author":"Mazor","year":"2015","journal-title":"J. Immunol. Methods"},{"key":"2023012712320334100_btx589-B31","doi-asserted-by":"crossref","first-page":"1881","DOI":"10.1002\/jcc.23330","article-title":"High\u2013quality protein backbone reconstruction from alpha carbons using Gaussian mixture models","volume":"34","author":"Moore","year":"2013","journal-title":"J. Comput. Chem"},{"key":"2023012712320334100_btx589-B32","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem"},{"key":"2023012712320334100_btx589-B33","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1038\/nature02055","article-title":"The DNA sequence and analysis of human chromosome 6","volume":"425","author":"Mungall","year":"2003","journal-title":"Nature"},{"key":"2023012712320334100_btx589-B34","doi-asserted-by":"crossref","first-page":"33.","DOI":"10.1186\/s13073-016-0288-x","article-title":"NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets","volume":"8","author":"Nielsen","year":"2016","journal-title":"Genome Med"},{"key":"2023012712320334100_btx589-B35","doi-asserted-by":"crossref","first-page":"177","DOI":"10.7326\/0003-4819-149-3-200808050-00241","article-title":"Systematic review: T-cell\u2013based assays for the diagnosis of latent tuberculosis infection: an update","volume":"149","author":"Pai","year":"2008","journal-title":"Ann. Intern. Med"},{"key":"2023012712320334100_btx589-B36","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.molimm.2013.04.011","article-title":"Accurate structure prediction of peptide\u2013MHC complexes for identifying highly immunogenic antigens","volume":"56","author":"Park","year":"2013","journal-title":"Mol. Immunol"},{"key":"2023012712320334100_btx589-B37","doi-asserted-by":"crossref","first-page":"163","DOI":"10.4049\/jimmunol.152.1.163","article-title":"Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains","volume":"152","author":"Parker","year":"1994","journal-title":"J. Immunol"},{"key":"2023012712320334100_btx589-B38","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1471-2105-6-132","article-title":"Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method","volume":"6","author":"Peters","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012712320334100_btx589-B39","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1093\/bioinformatics\/btg247","article-title":"Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules","volume":"19","author":"Peters","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012712320334100_btx589-B40","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1038\/nrd2224","article-title":"More than one reason to rethink the use of peptides in vaccine design","volume":"6","author":"Purcell","year":"2007","journal-title":"Nat. Rev. Drug Discov"},{"key":"2023012712320334100_btx589-B41","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s002510050595","article-title":"SYFPEITHI: database for MHC ligands and peptide motifs","volume":"50","author":"Rammensee","year":"1999","journal-title":"Immunogenetics"},{"key":"2023012712320334100_btx589-B42","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1007\/BF00172063","article-title":"MHC ligands and peptide motifs: first listing","volume":"41","author":"Rammensee","year":"1995","journal-title":"Immunogenetics"},{"key":"2023012712320334100_btx589-B43","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1002\/prot.22716","article-title":"Sub-angstrom modeling of complexes between flexible peptides and globular proteins","volume":"78","author":"Raveh","year":"2010","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712320334100_btx589-B44","doi-asserted-by":"crossref","first-page":"e1002404.","DOI":"10.1371\/journal.pcbi.1002404","article-title":"Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex","volume":"8","author":"Reboul","year":"2012","journal-title":"PLoS Comput. Biol"},{"key":"2023012712320334100_btx589-B45","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/S0198-8859(02)00432-9","article-title":"Prediction of MHC class I binding peptides using profile motifs","volume":"63","author":"Reche","year":"2002","journal-title":"Hum. Immunol"},{"key":"2023012712320334100_btx589-B46","doi-asserted-by":"crossref","first-page":"18413","DOI":"10.1038\/srep18413","article-title":"DockTope: a Web-based tool for automated pMHC-I modelling","volume":"5","author":"Rigo","year":"2015","journal-title":"Sci. Rep"},{"key":"2023012712320334100_btx589-B47","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1002\/bit.25554","article-title":"Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads","volume":"112","author":"Salvat","year":"2015","journal-title":"Biotechnol. Bioeng"},{"key":"2023012712320334100_btx589-B48","doi-asserted-by":"crossref","first-page":"843.","DOI":"10.1007\/s00249-011-0700-9","article-title":"Definition and testing of the GROMOS force-field versions 54A7 and 54B7","volume":"40","author":"Schmid","year":"2011","journal-title":"Eur. Biophys. J"},{"year":"2015","author":"Schrodinger","key":"2023012712320334100_btx589-B49"},{"key":"2023012712320334100_btx589-B50","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/17.12.1236","article-title":"ProPred: prediction of HLA-DR binding sites","volume":"17","author":"Singh","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012712320334100_btx589-B51","doi-asserted-by":"crossref","first-page":"e1000763.","DOI":"10.1371\/journal.pcbi.1000763","article-title":"Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model","volume":"6","author":"Ting","year":"2010","journal-title":"PLoS Comput. Biol"},{"key":"2023012712320334100_btx589-B52","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1002\/prot.20859","article-title":"Optimal design of protein docking potentials: efficiency and limitations","volume":"62","author":"Tobi","year":"2005","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712320334100_btx589-B53","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1002\/(SICI)1097-0134(20000701)40:1<71::AID-PROT90>3.0.CO;2-3","article-title":"On the design and analysis of protein folding potentials","volume":"40","author":"Tobi","year":"2000","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023012712320334100_btx589-B54","doi-asserted-by":"crossref","first-page":"446.","DOI":"10.1186\/1471-2105-12-446","article-title":"POPISK: T-cell reactivity prediction using support vector machines and string kernels","volume":"12","author":"Tung","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012712320334100_btx589-B55","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","author":"Vita","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012712320334100_btx589-B56","doi-asserted-by":"crossref","first-page":"3346","DOI":"10.1021\/acs.jctc.5b00179","article-title":"Rapid, precise, and reproducible prediction of peptide\u2013MHC binding affinities from molecular dynamics that correlate well with experiment","volume":"11","author":"Wan","year":"2015","journal-title":"J. Chem. Theory Comput"},{"key":"2023012712320334100_btx589-B57","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-0366-5_1","article-title":"Protein structure modeling with MODELLER","volume":"1137","author":"Webb","year":"2014","journal-title":"Protein Struct. Predict"},{"key":"2023012712320334100_btx589-B58","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1097\/TP.0b013e31823cab44","article-title":"Mechanisms of rejection: current perspectives","volume":"93","author":"Wood","year":"2012","journal-title":"Transplantation"},{"key":"2023012712320334100_btx589-B59","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1006\/jmbi.1998.2401","article-title":"Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation","volume":"285","author":"Word","year":"1999","journal-title":"J. Mol. Biol"},{"key":"2023012712320334100_btx589-B60","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1111\/cas.12050","article-title":"Next-generation peptide vaccines for advanced cancer","volume":"104","author":"Yamada","year":"2013","journal-title":"Cancer Sci"},{"key":"2023012712320334100_btx589-B61","doi-asserted-by":"crossref","first-page":"6981","DOI":"10.1073\/pnas.1018165108","article-title":"Large-scale characterization of peptide-MHC binding landscapes with structural simulations","volume":"108","author":"Yanover","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712320334100_btx589-B62","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/j.chembiol.2015.04.017","article-title":"Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo","volume":"22","author":"Zhao","year":"2015","journal-title":"Chem. Biol"},{"key":"2023012712320334100_btx589-B63","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1755-8794-1-18","article-title":"Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses","volume":"1","author":"Zvi","year":"2008","journal-title":"BMC Med. Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/3\/469\/48913049\/bioinformatics_34_3_469.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/3\/469\/48913049\/bioinformatics_34_3_469.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:19:27Z","timestamp":1674825567000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/3\/469\/4160677"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,18]]},"references-count":63,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2018,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx589","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,2,1]]},"published":{"date-parts":[[2017,9,18]]}}}