Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

In silico HLA-A2 restricted human ApoB100 CD8 T cell epitope prediction

FS Frank H. Schaftenaar
JA Jacob Amersfoort
HD Hidde Douna
MK Mara J. Kröner
AF Amanda C. Foks
IB Ilze Bot
BS Bram A. Slütter
GP Gijs H. M. van Puijvelde
JD Jan W. Drijfhout
JK Johan Kuiper
request Request a Protocol
ask Ask a question
Favorite

With use of the immune epitope database and analysis resource (iedb.org), putative human ApoB100 derived HLA-A2 restricted CD8 T cell epitopes were predicted. First top 1% predicted binders were selected using NetMHCpan29 which was reported to be the best prediction model for HLA-A264. Thereafter the Proteasomal cleavage/TAP transport/MHC class I combined predictor was used to rank the remaining peptides based on proteasomal cleavage and TAP transport26,27 and a consensus binding prediction28 combining Artificial neural network (ANN)31–34, Stabilized matrix method (SMM)30, and Scoring Matrices derived from Combinatorial Peptide Libraries (CombLib) models35. The 6 top peptides were synthesized (IHB, Leiden University Medical Centre).

Copyright and License information: The Author(s) ©2019
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A