Molecular Visualization Tools
From DrugPedia: A Wikipedia for Drug discovery
Molecular visualization programs are available on many platforms. They allow users to visualize and manipulate molecular structures.
[edit] Free molecular visualization tools
| Name | Description | Platform | Link |
|---|---|---|---|
| BioEditor | A tool for creating and viewing dynamic, formatted structure annotations | Windows | Download |
| canDo Shockwave 3D PDB Viewer | Free, easy to use tool for viewing molecular structures through a Web page--streams data directly from PDB | Mac (PPC or OS X), Windows | |
| Chemscape Chime | From MDL Information Systems. This program allows visualisation of structures | Windows, Macintosh (with Netscape 4.x only), and (as version 0.9z) SGI/Irix | Download |
| Chimera | Interactive molecular modeling system, free to academic/non-profit; displays multiple sequence alignments and associated structures, atom-type and H-bond identification, molecular dynamics trajectories (AMBER format), and offers ligand-screening interface (DOCK), filter by number/position of H-bonds, and extensibility to create custom modules | Windows, Linux, Mac OS X, IRIX, and Tru64 Unix | Home |
| Cn3D | Simultaneously displays structure, sequence, and alignment, with annotation and alignment editing features, for use with 3-D structures from NCBI's Entrez | Windows, Macintosh, and Unix | Download |
| iMol | Open GL graphics program displays small, large, and multiple molecules; measures distances and angles, superimposes structures, calculates RMSD between atom coordinates, structurally aligns chains, and displays dynamics trajectories. | For Mac OS X incl. 10.2 | Home |
| Java3D Molecular Visualisastion System | Free Java/Java3D program and source code | Windows or Unix | Download |
| Jmol | Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry | Windows, Mac OS X, and Linux/Unix systems | Home |
| Mage and Kinemages | Interactive molecular display for research and educational uses | Windows and Mac (OSX or PPC), Unix, and Linux | Home |
| MOLMOL | A program for displaying, analyzing, and manipulating the 3-D structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR | Mac OSX, Windows, Unix, Linux | Documentation |
| MolScript | A program for displaying structures in both detailed and schematic formats and writing images in various formats | Unix | Home |
| MolView and MolView Lite | Free molecular visualization programs | Mac | Download |
| PDB2MGIF | Free, user-friendly server that converts PDB files to animated gif files that can be used in Web pages and presentations. | Mac OSX, Windows, Unix, Linux | Documentation |
| PocketMol | Program to view and manipulate PDB files | PocketPC or handheld device running Windows CE 3.0 or higher | Download |
| ProteinScope | Free viewer to display and manipulate PDB files and create animations and slides of proteins | Windows | Home |
| PyMOL | A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. | Windows, Mac OSX, Unix, and Linux | Home |
| QmolA | lightweight OpenGL based molecular viewer | Windows | Home |
| RasMol | A free viewing system for PDB coordinate files | Mac PPC, Windows, Unix, and Linux systems | Download |
| Raster3D | A set of tools for generating high quality raster images of proteins or other molecules | Mac OSX, Windows, Unix, and Linux | Download |
| RasTop (v. 2.0) | A free user-friendly graphical interface to RasMol molecular visualization software (v. 2.7.2.1) | Windows and Linux | Download |
| Ribbons | A program for molecular illustration and error analysis | Mac OSX, Windows, Unix, and Linux | Download |
| RmscopII | A Tcl/Tk script responsible to redirect PDB files or RasMol scripts to multiple RasMol sessions; can be used as a Web browser helper application or as a standalone program | Mac (OSX or PPC), Windows, or Unix | Download |
| Swiss PDB viewer | A 3D graphics and molecular modeling program for the simultaneous analysis of multiple models and for model-building into electron density maps | Mac (OSX or PPC), Windows, Linux, or SGI | Download |
| Uppsala Electron Density Server | Generated density maps | Windows | Server |
| VMD (Visual Molecular Dynamics) | VMD provides visualization, analysis, and Tcl/Python scripting features, and has recently added sequence browsing and volumetric rendering features | MacOS X, and several versions of Unix and Windows | Download |
| WebMol | A Java PDB Viewer. WebMol was designed to display and analyze structural information contained in the Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application | Mac OSX, Windows, Unix, and Linux | Download |
| WebLab(TM) Viewer | software tool for visualizing molecules and communicating molecular information to colleagues | Windows and Mac | Documentation |
| DisMol applet | java based visualisation tool | Windows | Download |
| OpenAstexViewer | a Java molecular graphics program that assists in structure based drug design | Windows | Web Page |
