Israel Science and Technology Directory

Biomedical directorySoftware

The list below includes free software for 3D molecular visualization.
Also see: 2D Chemical Drawing Software.

Molecular Graphics Visualization Software
3DNASoftware programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
AbaloneWBiomolecular dynamics simulations of proteins, DNA, ligands.
AutoDockAutomated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
ChimeraXLVisualization and analysis of molecular structures including density maps, trajectories, and sequence alignments.
Cn3DLWSimultaneously displays structure, sequence and alignment. Based on NCBI MMDB database. Does not read PDB files.
Discovery Studio (DS) VisualizerLWProvides publication quality images with hierarchical presentation of chemical structure.
ICM-BrowserLWMolecule visualization, display ligand binding pocket surfaces, hydrogen bond display, measure distances.
JmolLWOpen-source Java viewer for chemical structures in 3D.
MOLMOLLWMolecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, especially protein and DNA.
NOCLWMolecular explorer for protein structure visualization, crystallographic mapping, modeling and refinement.
Protein Explorer (RasMol)LWMolecular visualization software for looking at macromolecular structure and its relation to function.
ProteinShaderProgram with ability to render a protein as a cartoon-style drawing that approximates what an artist might create by hand using pen and ink.
PyMOLLWMolecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
QuteMolWGenerates high resolution antialiased snapshots for publication quality renderings. Requires a graphics card.
Ramachandran Plot ExplorerWOutstanding software to visualize and manipulate phi and psi angles of peptide bonds.
RasTopLWMolecular visualization software adapted from the program RasMol.
Swiss-PdbViewerLWMolecular 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.
VMDLWMolecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
YasaraLWMolecular-graphics, modeling and simulation program powered by PVL (Portable Vector Language).
iMolMolecular visualization application for Mac OS X operating system.