ddhmed/peptide-physchem repository overview

⁠Peptide Physicochemical Property Calculator

This Docker image provides a lightweight and high-performance tool for calculating physicochemical properties of peptide sequences. The implementation is adapted from and optimized based on the algorithms provided by the R package Peptides (https://github.com/dosorio/Peptides⁠), with computationally intensive components reimplemented and accelerated for large-scale peptide analysis.

It accepts peptide sequences in FASTA format and supports efficient batch processing with multi-threading. Compared with the original R-based workflow, the optimized implementation is designed to substantially reduce computational overhead while preserving the underlying physicochemical calculation principles.

The tool calculates multiple commonly used peptide physicochemical descriptors, including molecular weight, isoelectric point (pI), hydrophobicity, instability-related properties, and other sequence-derived features. Results are exported in a tabular format for convenient downstream analysis.

The Docker image is intended for reproducible, portable, and high-throughput peptide analysis and can be readily integrated into bioinformatics pipelines, benchmarking workflows, and large-scale peptide screening applications.

⁠Reference implementation:

R package Peptides: https://github.com/dosorio/Peptides⁠

⁠Example usage:

docker pull ddhmed/peptide-physchem:20260818

docker run --rm -v "$PWD:/data" ddhmed/peptide-physchem:20260818 -help

docker run --rm -v "$PWD:/data" ddhmed/peptide-physchem:20260818 -i /data/peptides.fasta -o /data/result.tsv -m all -t 16

# where -i specifies the input FASTA file, -o specifies the output table, -m all calculates all supported physicochemical properties, and -t controls the number of CPU threads.