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PROTEOMICS.md

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Proteomics

General Resources for Protein Omics

Contents

Tool

  • alphafold - AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence. It regularly achieves accuracy competitive with experiment.
  • alphapept - A modular, python-based framework for mass spectrometry. Powered by nbdev.
  • matchms - Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.
  • pwiz - The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.

Datasets

  • PyPDB - A Python 3 toolkit for performing searches with the RCSB Protein Data Bank (PDB).

Visualization

  • Protael
  • ProteinPaint
  • pViz - pViz.js: a dynamic JavaScript & SVG library for visualization of protein sequence features
  • Aquaria
  • nightingale/protvista - Nightingale is a library of re-usable data visualisation Web Components, which can be used to display protein sequence features (ProtVista), variants, interaction data, 3D structure, etc.