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Leveraging Different Distance Functions to Predict Antiviral Peptides with Geometric Deep Learning from ESMFold-Predicted Tertiary Structures
(MDPI AG, 2026)
Cordoves-Delgado, Greneter
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García-Jacas, César R.
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Marrero Ponce, Yovani
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Aguila, Sergio A.
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Lizama-Uc, Gabriel
Background: Machine learning models have been shown to be a time-saving and cost-effective tool for peptide-based drug discovery. In this regard, different graph learning-driven frameworks have been introduced to exploit graph representations derived from predicted peptide structures. Such graphs are always derived by applying a Euclidean distance threshold between amino acid pairs, despite the fact that there is no evidence other than intuitive reasoning that supports the Euclidean distance as the most suitable. Objective: In this work, we examined the use of different distance functions to derive graph representations from predicted peptide structures to train deep graph learning-based models to predict antiviral peptides. Methods: To this end, we first analyzed how differently the closeness of the amino acids is characterized by different distance functions. Then, we studied the similarity between the graphs derived with several distance functions, as well as between them and random graphs. Finally, we trained several models with the best graph representations and analyzed how different they are regarding their predictions. Comparisons regarding state-of-the-art models were also performed. Results and Conclusion: We demonstrated that only using Euclidean distance thresholds is not sufficient criterion to build graphs representing structural features of predicted peptide structures, since other distance functions enabled building dissimilar graphs codifying different chemical spaces, which were useful in the construction of better discriminative models. ©The authors ©MDPI.
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StarPepWeb: an integrative, graph-based resource for bioactive peptides
(Oxford University Press, 2024)
López, Christian
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Cárdenas, Roberto
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Aguilera-Mendoza, Longendri
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Agüero-Chapin, Guillermin
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Martínez Ríos, Félix Orlando
Motivation: The rapid growth of bioactive peptide sequences presents challenges for organization and analysis. Existing repositories often specialize in functions, taxonomic origins, or structural classes, but most remain isolated, use heterogeneous metadata, and lack uniform descriptors or structural models. Few integrative web services exist, offering only partial coverage or depth. As a result, reproducible and comprehensive exploration of the bioactive peptide landscape remains limited, underscoring the need for a unified, source-tracked, extensible platform. Results: We present StarPepWeb, a freely accessible web application that democratizes access to StarPepDB, one of the largest curated repositories of bioactive peptides. The platform integrates 45 120 non-redundant sequences from 40 public databases into a source-tracked graph enriched with metadata, physicochemical features, and predicted 3D structures from ESMFold. Each peptide is represented with ESM-2 embeddings and iFeature descriptors, while the interface supports metadata-aware filtering, alignment-based similarity searches with single and multiple queries, and interactive visualization. A microservice-oriented architecture ensures scalability, maintainability, and reproducible versioned downloads, including Neo4j exports. StarPepWeb thus overcomes deployment and expertise barriers of the standalone database, providing an extensible, cloud-hosted framework for integrative bioactive peptide analysis. ©The authors ©Oxford University Press.
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Optimal Descriptor Subset Search via Chemical Information and Target Activity-Guided Algorithm for Antimicrobial Peptide Prediction
(American Chemical Society (ACS), 2025)
García-González, Luis A.
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Marrero Ponce, Yovani
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García-Jacas, César R.
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Aguila Puentes, Sergio A.
Antimicrobial peptides (AMPs) have emerged as a promising alternative to conventional drugs due to their potential applications in combating multidrug-resistant pathogens. Various computational approaches have been developed for AMP prediction, ranging from shallow learning methods to advanced deep learning techniques. Additionally, the performance of shallow learning models based on self-learning features derived from protein language models has recently been studied. However, the performance of AMP models based on shallow learning strongly depends on the quality of descriptors derived via manual feature engineering, which may miss crucial information by assuming that the initial descriptor set fully captures relevant information. The AExOp-DCS algorithm was introduced as an automatic feature domain optimization method that identifies the “optimal” descriptor set driven by the chemical structure and biological activity of the compounds under study. QSAR models built on AExOp-DCS optimized descriptors outperform those using nonoptimized sets. In this study, we explore the use of AExOp-DCS to identify optimal descriptor subsets for AMP modeling. Experimental results show that the descriptors returned by AExOp-DCS contain information comparable to those used in top-performing models while exhibiting higher discriminative capacity. The generated models based on the descriptors returned by AExOp-DCS achieved performance metric values comparable to state-of-the-art approaches while utilizing fewer descriptors, suggesting a more efficient modeling process. By reducing dimensionality without sacrificing accuracy, this approach contributes to the development of more efficient computational pipelines for AMP discovery. Finally, a Java software called AExOp-DCS-SEQ is freely available, enabling researchers to leverage its capabilities for peptide descriptor search and AMP classification tasks. ©The authors ©American Chemical Society (ACS) © Journal of Chemical Information and Modeling.

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