Peptide cheminformatics tools: making computational tasks accessible in peptide drug discovery

Peptides are versatile molecules with a growing relevance in addressing previously untreatable and complex diseases and targets. Computational methods offer powerful strategies to streamline peptide drug discovery by accelerating design-test cycles and guiding efforts toward promising candidates. The application of such tools requires specialized knowledge in informatics, programming, and statistics, with a growing number of computational tools and frameworks becoming available. In this review, we provide an overview of current computational approaches in peptide research, covering different phases of the computational pipeline, such as representation, similarity assessments, machine/deep learning (ML/DL) models, and peptide design. We further highlight available peptide cheminformatics tools based on their key features to facilitate their integration into peptide drug discovery pipelines.