The list below includes free software for 3D molecular visualization.
Also see: 2D Chemical Drawing Software.
| Software | Linux | Windows | Description |
|---|---|---|---|
| 3DNA | Software programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures | ||
| Abalone | W | Biomolecular dynamics simulations of proteins, DNA, ligands. | |
| AutoDock | Automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | ||
| ChimeraX | L | Visualization and analysis of molecular structures including density maps, trajectories, and sequence alignments. | |
| Cn3D | L | W | Simultaneously displays structure, sequence and alignment. Based on NCBI MMDB database. Does not read PDB files. |
| Discovery Studio (DS) Visualizer | L | W | Provides publication quality images with hierarchical presentation of chemical structure. |
| ICM-Browser | L | W | Molecule visualization, display ligand binding pocket surfaces, hydrogen bond display, measure distances. |
| Jmol | L | W | Open-source Java viewer for chemical structures in 3D. |
| MOLMOL | L | W | Molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, especially protein and DNA. |
| NOC | L | W | Molecular explorer for protein structure visualization, crystallographic mapping, modeling and refinement. |
| Protein Explorer (RasMol) | L | W | Molecular visualization software for looking at macromolecular structure and its relation to function. |
| ProteinShader | Program with ability to render a protein as a cartoon-style drawing that approximates what an artist might create by hand using pen and ink. | ||
| PyMOL | L | W | Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. |
| QuteMol | W | Generates high resolution antialiased snapshots for publication quality renderings. Requires a graphics card. | |
| Ramachandran Plot Explorer | W | Outstanding software to visualize and manipulate phi and psi angles of peptide bonds. | |
| RasTop | L | W | Molecular visualization software adapted from the program RasMol. |
| Swiss-PdbViewer | L | W | Molecular graphics with interface allowing analysis of several proteins at the same time. Can also read electron density maps, and provides tools to build into the density. |
| VMD | L | W | Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. |
| Yasara | L | W | Molecular-graphics, modeling and simulation program powered by PVL (Portable Vector Language). |
| iMol | Molecular visualization application for Mac OS X operating system. |