AMP Atlas: A Browser-Only Workbench for Antimicrobial Peptide Exploration and Interactive Helical-Wheel Design

Truong-Son Hy

Department of Computer Science, University of Alabama at Birmingham, United States

arXiv preprint · · arXiv:2610.29096 [cs.CE]

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Abstract

Accessible research software can connect published antimicrobial peptide (AMP) records to sequence analysis, molecular visualization, and interactive design without requiring a dedicated application server. We present AMP Atlas, an open-source, browser-only workbench that combines a DRAMP-derived database with local physicochemical calculations, published-neighbor retrieval, and sequence-guided structural comparison. The reported snapshot contains 12,784 source records, 10,579 canonical records, 5,183 source SMILES annotations, and 433 PDB chain structures. An inverse helical-wheel editor lets users specify peptide length, fill residues gradually, and immediately retrieve exact-length database matches under positional and property constraints. Selected-position residue frequencies support further editing while preserving the remaining constraints. A Web Worker performs searches and numerical calculations; a WebGL viewer provides interactive molecular representations. The static distribution occupies 138.8 MB and supports GitHub Pages hosting. Verification includes 23 Python tests, 30 browser-core/worker checks, a designer DOM integration suite, and agreement against fixed numerical references. This report describes the implemented algorithms and assumptions; it does not establish predictive accuracy for antimicrobial activity or experimentally validate designed peptides. The website is available at https://hysonlab.github.io/amp-atlas/, and the source code and database are available at https://github.com/HySonLab/amp-atlas.

Cite this report

Hy, Truong-Son. (2026). AMP Atlas: A Browser-Only Workbench for Antimicrobial Peptide Exploration and Interactive Helical-Wheel Design. arXiv:2610.29096 [cs.CE].

BibTeX citation
@misc{hy2026ampatlasbrowseronlyworkbench,
      title={AMP Atlas: A Browser-Only Workbench for Antimicrobial Peptide Exploration and Interactive Helical-Wheel Design},
      author={Truong-Son Hy},
      year={2026},
      eprint={2610.29096},
      archivePrefix={arXiv},
      primaryClass={cs.CE},
      url={https://arxiv.org/abs/2610.29096},
}

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