biostudies-literatureMartinez-Mauricio KLConsejo Nacional de Ciencia y Tecnologíae4928https://www.ebi.ac.uk/biostudies/studies/S-EPMC10949403biostudies-literatureUnknown33(4)Molecular features play an important role in different bio-chem-informatics tasks, such as the Quantitative Structure-Activity Relationships (QSAR) modeling. Several pre-trained models have been recently created to be used in downstream tasks, either by fine-tuning a specific model or by extracting features to feed traditional classifiers. In this regard, a new family of Evolutionary Scale Modeling models (termed as ESM-2 models) was recently introduced, demonstrating outstanding results in protein structure prediction benchmarks. Herein, we studied the usefulness of the different-dimensional embeddings derived from the ESM-2 models to classify antimicrobial peptides (AMPs). To this end, we built a KNIME workflow to use the same modeling methodology across experiments in order to guaranteeProtein science : a publication of the Protein SocietyExamining evolutionary scale modeling-derived different-dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow.PMC10949403320658Martinez-Mauricio KLCordoves-Delgado GGarcia-Jacas CRfalseExamining evolutionary scale modeling-derived different-dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow.Molecular features play an important role in different bio-chem-informatics tasks, such as the Quantitative Structure-Activity Relationships (QSAR) modeling. Several pre-trained models have been recently created to be used in downstream tasks, either by fine-tuning a specific model or by extracting features to feed traditional classifiers. In this regard, a new family of Evolutionary Scale Modeling models (termed as ESM-2 models) was recently introduced, demonstrating outstanding results in protein structure prediction benchmarks. Herein, we studied the usefulness of the different-dimensional embeddings derived from the ESM-2 models to classify antimicrobial peptides (AMPs). To this end, we built a KNIME workflow to use the same modeling methodology across experiments in order to guarantee2024-01-01T00:00:00Z2024 Apr2025-04-04T09:07:21.406Z2025-04-04T09:07:21.406ZS-EPMC109494033850151110.1002/pro.4928