Cheminformatics Molecular Visualization Tools and Sites
Guides to Molecular Visualization Tools
- World Index of Molecular Visualization Resources
- World Index of BioMolecular Visualization Resources
- NetSci's List of Molecular Mechanics and Molecular Dynamics Software
- Molecular Docking Web (Garrett M. Morris)
Chemical MIME
- Chemical Object Test Page at LLNL (includes information needed to configure browsers for chemical MIME types)
- The MIME Types
Selected Viewer and Plug-in Software
- Chemscape Chime (Elsevier MDL)
- Liz Dorland's Chemistry Tutorial and Resource Page (includes: "WWW Chemistry Tutorials Using the Chime Plugin")
- Molviz.org, Molecular Visualization Resources collected by Eric Martz (University of Massachusetts, Amherst)
- MDL Chime as a JCAMP-DX Data Viewer for Windows (for spectra)
- OpenRasMol Home Page
- RasMol Manual
- Molecular Visualization Freeware: Protein Explorer, Chime & RasMol (RasMol Home Page)
- ChemDraw Viewer (CambridgeSoft)
- ChemSketch (ACD Labs)
- Structure Drawing and Reporting - ChemWindow (BioRad)
- Cn3D (NCBI's free viewer for Entrez)
- Swiss-Pdb Viewer
- ISIS/Draw(Elsevier MDL)
- 3D Macromolecule Analysis and Kinemage Home Page at the Richardson Laboratory (Mage Software for Macintosh, PC, Linux and UNIX Platforms)
- Moviemol, An Easy-to-Use Molecular Display and Animation Program
- pyMOL
Selected Commercial Products
Converters of Chemical Structure Formats
- Open Babel
- BABEL; A Molecular Structure Information-Interchange Hub
- Mol2Mol
- Vega Online File Format Converter
- CLiDE (chemical literature data extraction tool from SimBioSys)
- ACD/ChemSketch
- Corina
Molecular Rendering Software
- Molecules in four dimensions (Mol4D)
- Frederick/Bethesda Data and Online Services
- The WWW PovChem Manual (Paul Thiessen)
- VMD: Visual Molecular Dynamics
- Molecular Modeling
- Ecce: Extensible Computational Chemistry Environment
Visualization Demonstration Sites
- BioMolecular Explorer 3D
- Common Molecules Collection (Indiana University Molecular Structure Center Reciprocal Net Project)
- History of visualization of biological macromolecules by Eric Martz and Eric Francoeur
- Chemical Object Test Page at Lawrence Livermore National Laboratory
- C4: Computers in Chemistry at Cabrillo College (includes a Chime Tutorial)
- WebMolecules: site designed for the 3D visualization of molecules.
- ChemVis
- Molecular Database without Transition Elements; Banque de molécules et d'ions ne contenant pas d'éléments de transition (by Gerard Dupuis)
- MathMol Library of 3-D Molecular Structures
- NCI-3D Database via Syncon
- NCI-3D Database via NIH Specialized Information Services
- ChemVIZ (Chemistry Visualization Program at NCSA)
- mineral web
- Virtual Museum of Minerals and Molecules
- Molecular Biophysics Images (Theoretical and Computational Biophysics Group, UIUC)
- Molecule of the Month
- Flick Coleman's Chime site at Wellesley
GIF Depictions
Unix
- XMView at the Indiana University Molecular Structure Center (will generate publication quality molecular graphics. Available for Red Hat Linux and SGI workstations)
Java and Javascript
- Jmol (for Windows, Mac OS X, and Linux/Unix systems) The JmolApplet is a web browser applet that can be integrated into web pages. The Jmol application is a standalone Java application that runs on the desktop. The JmolViewer is a development tool kit that can be integrated into other Java applications.
- JME Molecular Editor (Java applet to draw or edit molecules and reactions, including generation of substructure queries, and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures.)
- JaMM at the Indiana University Molecular Structure Center
- Marvin Java applets
VRML
- Cosmo Player VRML Plugin
- VRML Resources for Chemistry
- VRML File Creator for Chemical Structures Generation of VRML scenes from your 2D or 3D data files (supports over 40 structure file formats). Automatic generation of 3D coordinates if not contained in the input structure. Many display options to control the visual appearance.
- OrbVis is an online service for the calculation and visualization of molecular orbitals. The service will visualize all MOs of any reseonable structure you create. It employs a combination of a VRML2.0 plugin and a JAVA1.1 applet with many display options to control the visual appearance.