LitCovid-sentences  

PMC:7258756 / 10660-13148 JSONTXT 8 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T82 0-273 Sentence denotes Discontinuous epitopes on the modelled structure of the Indian case 1 SARS-CoV-2 spike protein were predicted using the online servers, Ellipro (http://tools.iedb.org/ellipro/) and DiscoTope 2.0 (http://tools.iedb.org/discotope/), integrated in the Immune Epitope Database.
T83 274-425 Sentence denotes Ellipro predicts epitopes based on the protusion index (PI), wherein the protein shape is approximated as an ellipsoid (Ref for Ellipro and DiscoTope).
T84 426-560 Sentence denotes An ellipsoid with the PI value of 0.8 indicates that 80 per cent of the residues are within the ellipsoid and 20 per cent are outside.
T85 561-642 Sentence denotes All residues that are outside the 80 per cent ellipsoid will have a score of 0.8.
T86 643-721 Sentence denotes Residues with larger scores are associated with greater solvent accessibility.
T87 722-761 Sentence denotes The PI value was set to a score of 0.8.
T88 762-906 Sentence denotes DiscoTope predicts epitopes using 3D structure and half-sphere exposure as a surface measure in a novel spatial neighbourhood definition method.
T89 907-1038 Sentence denotes Default values were set for sensitivity (0.47) and specificity (0.75) for selecting the amino acids forming discontinuous epitopes.
T90 1039-1264 Sentence denotes A sensitivity of 0.47 means that 47 per cent of the epitope residues are predicted as part of the epitopes, while a specificity of 0.75 means that 25 per cent of the non-epitope residues are predicted as part of the epitopes.
T91 1265-1418 Sentence denotes Outputs from both the methods were combined, and the final regions were mapped on the modelled 3D-structure as the most probable conformational epitopes.
T92 1419-1565 Sentence denotes In addition, we also predicted N-linked glycosylation sites in the S protein using NetNGlyc 1.0 Server (http://www.cbs.dtu.dk/services/NetNGlyc/).
T93 1566-1747 Sentence denotes The spike proteins were also screened for the presence of potential epitopes presented by major histocompatibility complex (MHC) class I molecules to cytotoxic T lymphocytes (CTLs).
T94 1748-1967 Sentence denotes The online NetCTL1.2 server (http://www.cbs.dtu.dk/services/NetCTL/) based on machine learning techniques such as artificial neural network (ANN) and support vector machine (SVM) was used to predict the T-cell epitopes.
T95 1968-2077 Sentence denotes The prediction was made for all the human leucocyte antigen (HLA) supertypes and the available human alleles.
T96 2078-2213 Sentence denotes The C terminal cleavage, weight of transport-associated protein (TAP) efficiency and threshold for identification were kept as default.
T97 2214-2354 Sentence denotes VaxiJen v2.0 tool was used to predict the antigenicity of the predicted epitopes (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html).
T98 2355-2488 Sentence denotes The sequences were further screened to be potential epitopes using the CTLPred online server (http://crdd.osdd.net/raghava/ctlpred/).