post-translational-modification

There are 3 repositories under post-translational-modification topic.

Villen-Lab / pyAscore
A python package for fast post translational modification localization, powered by Cython.
bioinformatics cpp cython post-translational-modification proteomics python
Language:Python 18
biodavidjm / artMS
Analytical R Tools for Mass Spectrometry
mass-spectrometry proteomics bioinformatics ap-ms phosphoproteomics quantitative-analysis bioconductor analytical analysis post-translational-modification
Language:R 14
Aksh77 / Bio-Scraper
Web scraper for UniProt and iPTMnet database
webscraping webscrapping uniprot iptmnet post-translational-modification protein-sequences beautifulsoup
Language:Python 10
wilhelm-lab / PROSPECT
Proteomics Mass Spectrometry Datasets for Machine Learning
annotations dataset deep-learning fragment-ions machine-learning mass-spectrometry peptide-sequences peptides post-translational-modification proteomics ptm retention-time spectrum
Language:Python 10
Vitek-Lab / MSstatsPTM
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments
proteomics post-translational-modification
Language:R 8
daniaki / pyPPI
A machine learning tool to assign edges in protein-protein interaction networks with a function.
bioinformatics post-translational-modification machine-learning protein-protein-interaction networks-biology
Language:Python 7
KarrLab / bpforms
Toolkit for concretely describing non-canonical DNA, RNA, and proteins
dna rna protein post-transcriptional-regulation post-translational-modification proteoform phosphorylation methylation epigenetics dna-damage crosslinks
Language:Python 6
eliza-m / CrossSpeciesWorkflow
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).
glycosylation lipid-modification sumoylation phosphorylation secondary-structure cell-localization acetylation post-translational-modification cwl-workflow cwl
Language:Python 5
frl21 / Phosphorylation_Prediction
This project is conduct research using deep learning to predict phosphorylation site in protein sequences
bioinformatics machine-learning protein-sequences post-translational-modification phosphorylation
Language:Jupyter Notebook 5
zfyuan / EpiProfile2.0_Family
EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data
epigenetics histone post-translational-modification mutations quantification
Language:MATLAB 4
VenkMallikarjun / BayesENproteomics
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.
proteomics matlab post-translational-modification
Language:MATLAB 3
VenkMallikarjun / BENPPy
Python implementation of BayesENproteomics with user-customised models and other additional features
python3 proteomics mcmc post-translational-modification
Language:Python 3
chinmayaNK22 / PTM-Site-Validator
Validation of modified amino acid sites in peptide sequences by identifying immonium ions in the raw spectra (.mgf format)
proteomics ptm-identification post-translational-modification
Language:Python 2
KCLabMTU / LMCrot
Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified Site Predictor
crotonylation natural-language-processing post-translational-modification protein-language-model protein-sequences transformers
Language:Python 2
PedroSeber / O-GlcNAcylation_Prediction
Code and datasets for the publication "Recurrent Neural Network-based Prediction of O-GlcNAcylation Sites in Mammalian Proteins"
artificial-intelligence artificial-neural-networks deep-learning glycosylation machine-learning post-translational-modification recurrent-neural-networks o-glycosylation
Language:Python 2
Vitek-Lab / MSstatsTMTPTM
R-based package for detecting differencially abundant post translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic experiments with tandem mass tag (TMT) labeling
mass-spectrometry proteomics msstats post-translational-modification
Language:R 2
bio2bel / phosphosite
biological-expression-language protein-modifications post-translational-modification
Language:Python 1
ChildrensMedicalResearchInstitute / ptm-visquant
Simple visualisation of PTM data sites alongside protein motif and family domain information
bioinformatics post-translational-modification ptm visualization
Language:JavaScript 1
DavisLaboratory / pyPPI
A machine learning tool to assign edges in protein-protein interaction networks with a function.
bioinformatics protein-protein-interaction machine-learning post-translational-modification networks-biology
Language:Python 1
Integrative-Transcriptomics / PTMVision
Web-application for Interactive Visualization of Post Translational Modifications
post-translational-modification proteomics visual-analytics web-application
Language:JavaScript 1
KCLabMTU / LMSuccSite
Improving Protein Succinylation Sites Prediction Using Features Extracted from Protein Language Model
plm post-translational-modification protein-language-model ptm-prediction succinylation-site-prediction embeddings succinylation
Language:Jupyter Notebook 1
PedroSeber / CHO_N-glycosylation_prediction
Code and datasets for the publication "Linear and Neural Network Models for Predicting N-glycosylation in Chinese Hamster Ovary Cells Based on B4GALT Levels"
artificial-intelligence artificial-neural-networks glycosylation machine-learning n-glycosylation post-translational-modification
Language:Jupyter Notebook 1
zfyuan / EpiProfileLite
One minute analysis of histone post-translational modifications by direct infusion mass spectrometry
epigenetics histone post-translational-modification direct-infusion one-minute-analysis
1
Citrullia-SDU / Citrullia
Software for the validation of citrullinated peptides
citrullination mass-spectrometry post-translational-modification posttranslational-modification
Language:C# 0
MolBIFFM / diana
data integration and network analysis of post-translational modification based on mass spectrometry data
post-translational-modification protein-protein-interaction-network
Language:Python 0
moritzmadern / SiteToProteinNormalization_in_MultiplexProteomics
Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference
algorithm isobaric-labeling post-translational-modification proteomics-data-analysis proteomics
Language:R 0
Pathmanaban / Scop3P-notebooks
Jupyter notebook examples of Scop3P REST API services
alphafold2 biophysics jupyter-notebook post-translational-modification protein-structure python3
Language:Jupyter Notebook 0
tairsha / taxa-specific-substitution-matrix
Algorithms for the generation of substitution matrices from intra-taxa variation data. Implemented and published on human genetic variation data.
amino-acids bioinformatics bioinformatics-algorithms bioinformatics-pipeline bioinformatics-tool biology genomics mutation-rate mutational-signatures phosphorylation post-translational-modification proteomics substitution-models
Language:Jupyter Notebook 0
maxperutzlabs-ms / SiteToProteinNormalization_in_MultiplexProteomics
Workflow to perform unbiased site-to-protein normalization in multiplex proteomics by accounting for ratio compression effects due to ion interference
algorithm isobaric-labeling post-translational-modification proteomics proteomics-data-analysis
Language:R

post-translational-modification

Villen-Lab / pyAscore

biodavidjm / artMS

Aksh77 / Bio-Scraper

wilhelm-lab / PROSPECT

Vitek-Lab / MSstatsPTM

daniaki / pyPPI

KarrLab / bpforms

eliza-m / CrossSpeciesWorkflow

frl21 / Phosphorylation_Prediction

zfyuan / EpiProfile2.0_Family

VenkMallikarjun / BayesENproteomics

VenkMallikarjun / BENPPy

chinmayaNK22 / PTM-Site-Validator

KCLabMTU / LMCrot

PedroSeber / O-GlcNAcylation_Prediction

Vitek-Lab / MSstatsTMTPTM

bio2bel / phosphosite

ChildrensMedicalResearchInstitute / ptm-visquant

DavisLaboratory / pyPPI

Integrative-Transcriptomics / PTMVision

KCLabMTU / LMSuccSite

PedroSeber / CHO_N-glycosylation_prediction

zfyuan / EpiProfileLite

Citrullia-SDU / Citrullia

MolBIFFM / diana

moritzmadern / SiteToProteinNormalization_in_MultiplexProteomics

Pathmanaban / Scop3P-notebooks

tairsha / taxa-specific-substitution-matrix

maxperutzlabs-ms / SiteToProteinNormalization_in_MultiplexProteomics