Visualization and modeling tools
- ePMV, mMaya, BioBlender enable to import various biological data into professional 3D tools:
- embedded Python Molecular Viewer (ePMV)
- Molecular Maya Toolkit (mMaya)
- 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