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.

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

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

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 modification, sumoylation, etc).

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"

No description provided.

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

Improving Protein Succinylation Sites Prediction Using Features Extracted from Protein Language Model

One minute analysis of histone post-translational modifications by direct infusion mass spectrometry

Simple visualisation of PTM data sites alongside protein motif and family domain information

Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference

Software for the validation of citrullinated peptides

data integration and network analysis of post-translational modification based on mass spectrometry data

Algorithms for the generation of substitution matrices from intra-taxa variation data. Implemented and published on human genetic variation data.