A python package for fast post translational modification localization, powered by Cython.

Proteomics Mass Spectrometry Datasets for Machine Learning

Analytical R Tools for Mass Spectrometry

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments

PSI-MOD ontology for modified and unmodified amino acid residues

Web scraper for UniProt and iPTMnet database

A machine learning tool to assign edges in protein-protein interaction networks with a function.

This project is conduct research using deep learning to predict phosphorylation site in protein sequences

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

CWL workflow that facilitate performing a series of structural and phenotype related third party prediction methods starting from either a protein FASTA file or a list of Uniprot IDs. Integrated prediction methods refer to secondary structure, solvent accessibility, disordered regions, PTS modifications (phosphorylation, glycosylation, lipid mod…

Web application for the interactive visualization and exploration of post-translational modifications of proteins from open and closed search software.

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data

Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified Site Predictor

Python implementation of BayesENproteomics with user-customised models and other additional features

Code and datasets for the publications "Predicting O-GlcNAcylation sites in mammalian proteins with transformers and RNNs trained with a new loss function" and "Recurrent Neural Network-based Prediction of O-GlcNAcylation Sites in Mammalian Proteins"

R-based package for detecting differencially abundant post translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic experiments with tandem mass tag (TMT) labeling

Non-linear Bayesian elastic net regression for calculating protein and PTM fold changes from peptide intensities in label-free, bottom-up proteomics on heterogeneous primary human samples.

Code and datasets for the publication "Linear and Neural Network Models for Predicting N-glycosylation in Chinese Hamster Ovary Cells Based on B4GALT Levels"

Validation of modified amino acid sites in peptide sequences by identifying immonium ions in the raw spectra (.mgf format)