Visualization and modeling tools

  • Qutemol offers several visual effects to provide a better perception of the 3D shape of a (single) protein
  • Molecular Flipbook allows to easily and rapidly create 3D animations. Available for Mac and Windows.
  • UnityMol is a molecular editor, viewer and prototyping platform based on the Unity3D game engine. Available for Mac, Windows, Linux. A webplayer can be used here.

DNA 3D modeling tools

  • 3DNAdesigner: downloadable program that researchers can use to model any sequence and have the ability to spatially constrain the ends. It let’s the user have the ability to bind proteins/ligands/drugs to any part of the sequence (see video)

Tutorials and 3D scenes for molecular biomodeling and viz


  • The Protein Model Portal: gives access to various protein models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment
    • Analysis, reconstruction and visualization of nucleic-acid structures: web3DNA
    • Prediction of large RNA 3D structures: RNA composer
  • Xwalk calculates Solvent Accessible Surface distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules.
  • MOLE locates and characterizes channels and pores in biomacromolecules.

Reconstruction of cells or organisms in virtual