The list below includes free software for 3D molecular visualization.
Also see: 2D Chemical Drawing Software.
To re-sort the list, click a column heading.
|3DNA||Software programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures|
|Abalone||W||Biomolecular dynamics simulations of proteins, DNA, ligands.|
|AstexViewer||L||W||Java molecular graphics program that can be used as an Applet in a web page or as a desktop application.|
|AutoDock||Automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.|
|Cn3D||L||W||Simultaneously displays structure, sequence and alignment. Based on NCBI MMDB database. Does not read PDB files.|
|DeepView||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.|
|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.|
|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.|