Getting started

Loading protein structures

• ESBTL → Efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules. Good integration with CGAL. (doi: 10.1093/bioinformatics/btq083) [C++]
• gemmi ★ → Library for reading and writing PDB and mmCIF files. Also has support for generating biological assemblies, applying basic transformations, performing structural alignment, calculating dihedral angles, etc.. [C++, Python]

Homology modeling

• MODELLER → Most-widely used homology modeling software. [Python, Proprietary]
• ProMod3 → A free and open source homollogy modeling toolbox powering the SWISS-MODEL server. Uses OPENMM for some refinement. [LGPL]
  ProMod3—A versatile homology modelling toolbox (2021)
• AlphaFold2...

Structural alignment

• Cealign - PyMol plugin.

Structural visualization

• 3Dmol.js → WebGL accelerated JavaScript molecular graphics library. The Jupyter widget works in Google Colab.
• LiteMol → A library/plugin for handling 3D structural molecular data (not only) in the browser.
• Mol* ★ → A comprehensive macromolecular library. Developed to combine and build on the strengths of LiteMol and NGL.
• NGL → WebGL protein viewer. There is also a Jupyterlab widget with bidirectional information flow.