ArticleJournal of cheminformatics2023
pyPept: a python library to generate atomistic 2D and 3D representations of peptides.
Article in Journal of cheminformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- PEP-EDIT: a web server for the 3D generation and interactive editing of complex peptides.Nucleic acids research · 2026Article
- Secondary-Structure-Dependent Cooperation and Interference Between Peptides of Different Chain Lengths in Antifreeze Activity: Insights from Molecular Dynamics Simulations.Foods (Basel, Switzerland) · 2026Article
- Helmkit: fast and robust conversion of HELM notation to atomistic representations for large-scale macromolecular informatics.Journal of cheminformatics · 2026Article
- Identification and Characterization of an In Silico Designed Membrane-Active Peptide with Antiviral Properties.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Peptide-Based Strategies AgainstPharmaceuticals (Basel, Switzerland) · 2025Review
- PepFuNN: Novo Nordisk Open-Source Toolkit to Enable Peptide in Silico Analysis.Journal of peptide science : an official publication of the European Peptide Society · 2025Article
- cyclicpeptide: a Python package for cyclic peptide drug design.Briefings in bioinformatics · 2024Article
- tracerDB: a crowdsourced fluorescent tracer database for target engagement analysis.Nature communications · 2024Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We present pyPept, a set of executables and underlying python-language classes to easily create, manipulate, and analyze peptide molecules using the FASTA, HELM, or recently-developed BILN notations. The framework enables the analysis of both pure proteinogenic peptides as well as those with non-natural amino acids, including support to assemble a customizable monomer library, without requiring programming. From line notations, a peptide is transformed into a molecular graph for 2D depiction tasks, the calculation of physicochemical properties, and other systematic analyses or processing pipelines. The package includes a module to rapidly generate approximate peptide conformers by incorporating secondary structure restraints either given by the user or predicted via pyPept, and a wrapper tool is also provided to automate the generation and output of 2D and 3D representations of a peptide directly from the line notation. HELM and BILN notations that include circular, branched, or stapled peptides are fully supported, eliminating errors in structure creation that are prone during manual drawing and connecting. The framework and common workflows followed in pyPept are described together with illustrative examples. pyPept has been released at: https://github.com/Boehringer-Ingelheim/pyPept .
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