Proteomics Mass Spectrometry Datasets for Machine Learning

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

Analytical R Tools for Mass Spectrometry

PSI-MOD ontology for modified and unmodified amino acid residues

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

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

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

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…

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)