Long short-term memory recurrent neural networks for learning peptide and protein sequences to later design new, similar examples.

Python framework for Deep Learning in Proteomics

Proteomics Mass Spectrometry Datasets for Machine Learning

A spectacularly simple package for working with peptide sequences.

Visualize alpha-helical peptide sequences in Python using helical wheels and wenxiang diagrams

Protein Cleaver is a versatile tool for protein analysis and digestion.

Script developed to transform the amino acid smiles to one letter code for later analysis

Using Python to locate a peptide sequence to a reference protein and PTM site

A de novo peptide sequencing transformer

Visualize alpha-helical peptide sequences in R using helical wheels and wenxiang diagrams. See https://doi.org/10.21105/joss.01008 for more details.

Modifications part of the Peptide modifications cycle

Predict and match digested peptides sequences, their mass m/z and MS/MS spectra with chemical derivatization or post-translational modification.

A peptide fragment ion calculator made with streamlit

Pmlbeta: a PyMOL extension for building β-amino acid insertions and β-peptide sequences. To cite this software publication: https://www.sciencedirect.com/science/article/pii/S2352711020303678

Miscellaneous Scripts in Bioinformatics

Python Code for Peptide Sequencing of plasma after Chlorine Exposure

Locates genomic and peptide sequences for biological analysis.

Given files with sequences containing signal peptides and sequences not containing signal peptides, multiple classifiers were tested to see which performs best in the classification of signal peptide sequences.

This is an early stage calculator that uses Python to automate the time-consuming calculation components necessary for solid phase peptide synthesis (SPPS). At its current version (v1), the calculator allows calculation of the molecular weight of a desired peptide sequence, the mass of solid support resin needed for SPPS and the percentage yield

This programs calculates the approximate energy (ATP) required to form a peptide chain