MMPred : a tool to predict peptide mimicry events in MHC class II recognition
Guerri, Filippo (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Junet, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Farrés, Judith (Anaxomics Biotech)
Daura i Ribera, Xavier (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")

Date:	2024
Abstract:	We present MMPred, a software tool that integrates epitope prediction and sequence alignment algorithms to streamline the computational analysis of molecular mimicry events in autoimmune diseases. Starting with two protein or peptide sets (e. g. , from human and SARS-CoV-2), MMPred facilitates the generation, investigation, and testing of mimicry hypotheses by providing epitope predictions specifically for MHC class II alleles, which are frequently implicated in autoimmunity. However, the tool is easily extendable to MHC class I predictions by incorporating pre-trained models from CNN-PepPred and NetMHCpan. To evaluate MMPred's ability to produce biologically meaningful insights, we conducted a comprehensive assessment involving i) predicting associations between known HLA class II human autoepitopes and microbial-peptide mimicry, ii) interpreting these predictions within a systems biology framework to identify potential functional links between the predicted autoantigens and pathophysiological pathways related to autoimmune diseases, and iii) analyzing illustrative cases in the context of SARS-CoV-2 infection and autoimmunity. MMPred code and user guide are made freely available at https://github. com/ComputBiol-IBB/MMPRED.
Grants:	European Commission 765158 European Commission 813545 Agencia Estatal de Investigación PID2019-111364RB-I00
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Molecular mimicry ; Epitope prediction ; Sequence alignment ; MHC class II ; Autoimmune disease ; SARS-CoV-2
Published in:	Frontiers in genetics, Vol. 15 (December 2024) , ISSN 1664-8021

DOI: 10.3389/fgene.2024.1500684
PMID: 39722794

15 p, 2.0 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
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