Dataset and Github repository

To find the datasets that were used for the evaluation/comparison of APE-Gen2.0 to other tools in the literature, as well as to access the code of APE-Gen2.0, please use the repo found here.

References

If you used our web-based tool, or used the APE-Gen2.0 docker image or source code, please cite [1].

This webserver uses the newest version of APE-Gen2.0 (previous reference), which is more accurate and easy-to-use than its predecessor, with expanded pMHC structural modeling repertoire to bout. If however, you would like to see/cite the original publication, use [2].

1. R. Fasoulis, M. M. Rigo, G. Lizée, D. A. Antunes, and L. E. Kavraki, “APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries,” Journal of Chemical Information and Modeling, vol. 64, no. 5, pp. 1730–1750, Mar. 2024.
   
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2. Abella JR, Antunes DA, Clementi C, Kavraki LE. APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. Molecules. 2019; 24(5):881. https://doi.org/10.3390/molecules24050881
   
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