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Side chain substitution benchmark for peptide/MHC interaction.
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2
Structural prediction of peptides binding to MHC class I molecules.
Proteins. 2006 Apr 1;63(1):43-52. doi: 10.1002/prot.20870.
3
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Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes.
PLoS Comput Biol. 2018 Nov 8;14(11):e1006457. doi: 10.1371/journal.pcbi.1006457. eCollection 2018 Nov.
8
Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition.
J Biol Chem. 2003 Jan 10;278(2):1281-90. doi: 10.1074/jbc.M206853200. Epub 2002 Oct 30.
10
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction.
BMC Bioinformatics. 2017 Dec 28;18(1):585. doi: 10.1186/s12859-017-1997-x.

引用本文的文献

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epiTCR-KDA: knowledge distillation model on dihedral angles for TCR-peptide prediction.
Bioinform Adv. 2024 Nov 29;4(1):vbae190. doi: 10.1093/bioadv/vbae190. eCollection 2024.
2
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.
Bioinformatics. 2016 Jan 15;32(2):181-6. doi: 10.1093/bioinformatics/btv502. Epub 2015 Sep 22.
6
Relaxation estimation of RMSD in molecular dynamics immunosimulations.
Comput Math Methods Med. 2012;2012:173521. doi: 10.1155/2012/173521. Epub 2012 Sep 16.
8
Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses.
J Comput Aided Mol Des. 2011 Oct;25(10):947-58. doi: 10.1007/s10822-011-9474-5. Epub 2011 Oct 1.
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PeptX: using genetic algorithms to optimize peptides for MHC binding.
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本文引用的文献

1
IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
Protein Sci. 2007 Jul;16(7):1294-307. doi: 10.1110/ps.062658307. Epub 2007 Jun 13.
3
Methods and protocols for prediction of immunogenic epitopes.
Brief Bioinform. 2007 Mar;8(2):96-108. doi: 10.1093/bib/bbl038. Epub 2006 Oct 31.
4
How TCRs bind MHCs, peptides, and coreceptors.
Annu Rev Immunol. 2006;24:419-66. doi: 10.1146/annurev.immunol.23.021704.115658.
5
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.
Proteins. 2006 May 15;63(3):512-26. doi: 10.1002/prot.20831.
6
Structural prediction of peptides binding to MHC class I molecules.
Proteins. 2006 Apr 1;63(1):43-52. doi: 10.1002/prot.20870.
7
All are not equal: a benchmark of different homology modeling programs.
Protein Sci. 2005 May;14(5):1315-27. doi: 10.1110/ps.041253405.
9
SCit: web tools for protein side chain conformation analysis.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W508-11. doi: 10.1093/nar/gkh388.
10
A graph-theory algorithm for rapid protein side-chain prediction.
Protein Sci. 2003 Sep;12(9):2001-14. doi: 10.1110/ps.03154503.

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