skills.rest
mims-harvard
mims-harvardOFFICIAL
Explore all skills by this author →
Website𝕏@marinkazitnikGitHub

tooluniverse-protein-modification-analysis

Analyzes protein post-translational modification sites, enzymes, and functional consequences using iPTMnet, ProtVar, and UniProt.

1.7k|254|Updated Mar 3, 2025
Search Tags:#proteomics#uniprot#protein analysis#PTM#phosphorylation#iptmnet#kinase-substrate
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-modification-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-protein-modification-analysis
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-protein-modification-analysis
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-modification-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Researchers studying protein regulation need to identify post-translational modification (PTM) sites, the enzymes responsible, and their functional or disease consequences, but this data is scattered across multiple specialized databases like iPTMnet, ProtVar, UniProt, and ELM.

Core Features & Use Cases

  • PTM Site Inventory: Retrieve phosphorylation, ubiquitination, acetylation, glycosylation, and methylation sites with enzyme and evidence annotations from iPTMnet.
  • Functional Context Grading: Assess the consequence of each PTM using ProtVar domain annotations, ELM linear motifs, and PTM-dependent protein interactions, graded on a T1-T4 evidence scale.
  • Use Case: Given a protein like TP53, resolve its UniProt accession, enumerate all known PTM sites and proteoforms, identify kinase-substrate relationships, and produce an evidence-graded report linking modifications to functional and disease annotations.

Quick Start

Analyze the phosphorylation sites of human TP53 and identify the kinases responsible and their functional consequences.

Frequently Asked Questions about tooluniverse-protein-modification-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find phosphorylation sites for a protein?▼

Resolve the protein to its UniProt accession, then call iPTMnet_get_ptm_sites with the accession to retrieve positions, residues, modification types, enzymes, and evidence. Group results by modification type for analysis.

What databases are used for PTM analysis?▼

The workflow uses iPTMnet as the primary source for PTM sites and enzymes, ProtVar for functional consequences, UniProt for baseline annotations, STRING for interactions, ELM for linear motifs, and MassIVE/ProteomeXchange for experimental mass spectrometry data.

How do I identify kinase-substrate relationships?▼

Use iPTMnet_search with the substrate role parameter to find candidates, then iPTMnet_get_ptm_sites returns the enzyme responsible for each modification site. PTM-dependent interactions are retrieved via iPTMnet_get_ptm_ppi.

What happens if a protein is not in iPTMnet?▼

Fall back to UniProt entry annotations for PTM and processing information. If PTM-PPI data is missing, use STRING general protein interactions, and if ProtVar lacks data, rely on UniProt domain annotations.

What are the limitations of iPTMnet PTM data?▼

iPTMnet is biased toward well-studied proteins, proteoform data covers only observed modification combinations, and PTM-PPI records include only PTM-specific evidence. Predicted sites without experimental validation are graded as tier T4.

Related Skills

Explore More Education & Research Skills→
MusserLabMusserLab
2

gene-lookup

Map gene IDs and protein accessions to gene symbols across biological databases.

Official
Intermediate
QSong-githubQSong-github
130

TarKG

Query drug-target relationships from a local TarKG TSV dataset.

Community
Intermediate
zongtingweizongtingwei
25

proteomics

Identify and quantify proteins from MS data with quality control and differential analysis.

Community
Advanced
gabrielvuksanigabrielvuksani

pyopenms

Analyze LC-MS mass spectrometry data with pyopenms for proteomics and metabolomics.

Community
Advanced