BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes

作者: Martin Closter Jespersen , Bjoern Peters , Morten Nielsen , Paolo Marcatili

DOI: 10.1093/NAR/GKX346

关键词: AntibodyProtein structureEpitopeBiologyAntigenSequence analysisComputational biologyRandom forestLinear epitopeSequence (medicine)

摘要: … In each complex, we identified the antibody molecules using HMM models developed elsewhere, and for each antibody we define its antigens as all the non-antibody protein chains that …

参考文章(25)
Michael Schantz Klausen, Mads Valdemar Anderson, Martin Closter Jespersen, Morten Nielsen, Paolo Marcatili, LYRA, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Research. ,vol. 43, ,(2015) , 10.1093/NAR/GKV535
J. Swets, Measuring the accuracy of diagnostic systems Science. ,vol. 240, pp. 1285- 1293 ,(1988) , 10.1126/SCIENCE.3287615
Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar, Predicting flexible length linear B-cell epitopes. computational systems bioinformatics. ,vol. 7, pp. 121- 132 ,(2008) , 10.1142/9781848162648_0011
Bent Petersen, Thomas Petersen, Pernille Andersen, Morten Nielsen, Claus Lundegaard, A generic method for assignment of reliability scores applied to solvent accessibility predictions BMC Structural Biology. ,vol. 9, pp. 51- 51 ,(2009) , 10.1186/1472-6807-9-51
Charles C. Bigelow, On the average hydrophobicity of proteins and the relation between it and protein structure Journal of Theoretical Biology. ,vol. 16, pp. 187- 211 ,(1967) , 10.1016/0022-5193(67)90004-5
Jens Vindahl Kringelum, Morten Nielsen, Søren Berg Padkjær, Ole Lund, Structural analysis of B-cell epitopes in antibody:protein complexes Molecular Immunology. ,vol. 53, pp. 24- 34 ,(2013) , 10.1016/J.MOLIMM.2012.06.001
Robert M. Sweet, David Eisenberg, Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure Journal of Molecular Biology. ,vol. 171, pp. 479- 488 ,(1983) , 10.1016/0022-2836(83)90041-4
Yasser EL‐Manzalawy, Drena Dobbs, Vasant Honavar, Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition. ,vol. 21, pp. 243- 255 ,(2008) , 10.1002/JMR.893
Rosella Mechelli, Renato Umeton, Claudia Policano, Viviana Annibali, Giulia Coarelli, Vito AG Ricigliano, Danila Vittori, Arianna Fornasiero, Maria Chiara Buscarinu, Silvia Romano, Marco Salvetti, Giovanni Ristori, International Multiple Sclerosis Genetics Consortium, Wellcome Trust Case Control Consortium, None, A “Candidate-Interactome” Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis PLoS ONE. ,vol. 8, pp. e63300- 9 ,(2013) , 10.1371/JOURNAL.PONE.0063300