Interactive browser tool connects antimicrobial peptides with design and visualization
AMP Atlas: A Browser-Only Workbench for Antimicrobial Peptide Exploration and Interactive Helical-Wheel Design
Computational Engineering, Finance, and Science
Summary
Finding new antimicrobial peptides, which are tiny proteins that can kill germs, helps develop new medicines. The authors made a free tool called AMP Atlas that runs entirely in a web browser, letting users search a large database of peptides and visualize their shapes interactively. You can also design new peptides by specifying patterns and immediately see exact matches from the database. This helps scientists and engineers explore peptide properties without installing special software.
What this means in practice
- •For bioinformatics developers: Build web-based tools for analyzing and designing antimicrobial peptides without backend servers using AMP Atlas’s browser-only approach.
- •For pharmaceutical peptide designers: Use AMP Atlas’s interactive helical wheel editor to create peptide sequences that meet specific positional and property constraints matching known antimicrobial peptides.
Authors
Truong-Son Hy
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