Structural Immunoinformatics
APE-Gen2.0
Increasing pMHC modeling accuracy
By adopting a hybrid modeling approach based on sampling scoring and template-based modeling, APE-Gen2.0 provides state-of-the-art pMHC structural modeling performance.
Expanding pMHC modeling repertoire
APE-Gen2.0 expands pMHC structural repertoire to previously difficult-to-model cases, such as peptides exhibiting post-translational modification, as well as to peptides that assume non-canonical geometries in the binding cleft.
Making pMHC structural modeling more accessible
To facilitate pMHC modeling, APE-Gen2.0 is provided as a webserver at this link.
Further Links
Check out our online web server here: Web server
Check out our github repo here: Github
You can find the paper here: Paper
See the ITCR connections with APE-Gen2.0 here: ITCR Connections
References
If you use APE-Gen2.0 in your work, please cite the tool as shown:
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.
J. R. Abella, D. A. Antunes, C. Clementi, and L. E. Kavraki, “APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations,” Molecules, vol. 24, no. 5, p. 881, 2019. PMID: 30832312, PMCID: PMC6429480