peptide-sequences

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

Parse ProForma 2.1 peptide sequences and calculate masses, fragments, and isotopic distributions in Python.

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

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

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

A de novo peptide sequencing transformer

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

A peptide fragment ion calculator made with streamlit

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

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

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

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

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

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

Miscellaneous Scripts in Bioinformatics

Locates genomic and peptide sequences for biological analysis.

A web application focuses on visualizing molecular docking results for peptide–protein interactions in a clear, interactive interface to support antiviral drug research