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 Python package for peptide sequence analysis built around ProForma 2.1 notation. Calculate masses, generate fragments, predict isotopic patterns, and more.

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

A Multi-Representation Ensemble Learning Framework for Accurate Bitter Peptide Identification

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

A de novo peptide sequencing transformer

A peptide fragment ion calculator made with streamlit

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

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

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

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

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

Modifications part of the Peptide modifications cycle

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

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples

Python Code for Peptide Sequencing of plasma after Chlorine Exposure

Miscellaneous Scripts in Bioinformatics