Next-generation IEDB tools: a platform for epitope prediction and analysis
Zhen Yan, Kevin Kim, Haeuk Kim, Brendan Ha, Anaïs Gambiez, Jason W. Bennett, Marcus Fabiano de Almeida Mendes, Raphael Trevizani, Jarjapu Mahita, Eve Richardson, Daniel Marrama, Nina Blazeska, Zeynep Koşaloğlu, Morten Nielsen, Alessandro Sette, Bjoern Peters, Jason Greenbaum
Abstract
The Next-Generation (NG) IEDB Tools website (https://nextgen-tools.iedb.org) provides users with a redesigned interface to many of the algorithms for epitope prediction and analysis that were originally released on the legacy IEDB Tools website. The initial release focuses on consolidation of all tools related to HLA class I epitopes (MHC binding, elution, immunogenicity, and processing), making all of these predictions accessible from a single application and allowing for their simultaneous execution with minimal user inputs. Additionally, the PEPMatch tool for identifying highly similar epitopes in a set of curated proteomes, as well as a tool for epitope clustering, are available on the site. The NG Tools site allows users to build data pipelines by sending the output of one tool as input for the next. Over the next several years, all pre-existing IEDB Tools, and any newly developed tools, will be integrated into this new site. Here we describe the philosophy behind the redesign and demonstrate the utility and productivity enhancements that are enabled by the new interface.