Structural Visualization and Manipulation of Biological Molecules

This section contains lists of free software and web applications that are designed to display large biomolecules. Links to additional information on each tool are provided, including program documentation (manual, tutorials, etc.)

• Standalone Applications
• Web Applications
• Web Services (no plugin or applets to install)

Our main tool for high-quality molecular graphics images and animations is PyMOL. PyMOL has excellent capabilities in creating high-quality images from 3-D structures and it has well developed functions for manipulating structures and some basic functions to analyze their chemical properties. The possibilities to write scripts and plugins as well as to incorporate PyMOL in custom software are vast and superior to most other programs.

Standalone Applications

open in new windowBALL View	BALLView is molecular viewer and modeling tool. It combines visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models.
open in new windowChimera	UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
open in new windowDeepView Swiss-PDB Viewer	DeepView Swiss PDB Viewer user-friendly molecular visualization program. It includes in addition various building and modeling tools.
open in new windowDino	DINO is a real time 3-D visualization program for structural biology data.
open in new windowDiscovery Studio Visualizer	DS (Discovery Studio) Visualizer is a cut-down version of a commercial DS viewer/editor-program sold by Accelrys, which is free and very user-friendly.
Friend	Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA.
open in new windowiMol	iMol is a molecular visualization application for Mac OS X operating system.
open in new windowJmol	Jmol is an open source molecular viewer written in Java. It can be used as applet which displays the molecule within a web browser or as standalone application.
open in new windowMGLTools	MGLTools is a software for visualization and analysis of molecular structures. It incude three main application: ADT, a graphical front-end for setting up and running AutoDock; PMV, molecular viewer and Vision, a visual-programming environment
open in new windowPyMOL	PyMOL is open-source molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
open in new windowVMD	VMD (Visual Molecular Dynamics) is a free molecular visualization program for displaying, animating, and analyzing large bimolecular systems using 3-D graphics and built-in scripting.

Web Applications

open in new windowCn3D	Cn3D is an open-source code visualization tool for biomolecular structures, sequences, and sequence alignments. Cn3D is typically run from a web browser as a helper application for NCBI's Entrez system.
Friend	Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA.
open in new windowJmol	Jmol is an open source molecular viewer written in Java. It can be used as applet which displays the molecule within a web browser or as standalone application.