Open Source viewer that includes features for morphing proteins and
visualization of lipophilic and electrostatic potentials.
A protein visualization and modeling program
Create beautiful publication quality images and movies. Users can superpose and analyse structures as well. The program runs 'out of the box' on Linux, MacOSX and Windows platforms.
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 - for Windows,
Linux, Mac OS X, IRIX, and Tru64 Unix
Simultaneously displays structure, sequence, and alignment, with
annotation and alignment editing features, for use with 3-D
structures from NCBI's Entrez; available for Windows, Macintosh,
A program for building, displaying and manipulating all kinds of
crystal and molecular structures.
Embedded Python Molecular Viewer (ePMV) is an open-source plug-in
that runs molecular modeling software directly inside of professional
3D animation applications
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.
Jmol is a free, open source molecule viewer for students,
educators, and researchers in chemistry and biochemistry. It is
cross-platform, running on Windows, Mac OS X, and Linux/Unix
Mage and Kinemages
molecular display for research and educational uses. Free, open
source for Windows and Mac (OSX or PPC), Unix, and Linux. A Java
version does 3-D Web display without plug-ins.
Marvin is a collection of tools for drawing, displaying and
characterizing chemical structures, queries, macromolecules and
reactions for all operating systems, web pages and custom
Interactively generate heterogeneous PDB-based membranes with varying lipid compositions and
semi-automatic protein placement. Supports membrane patches and vesicles, microdomains as well as stacking of
monolayer and/or bilayer membranes.
Molecule World 2.1 is an iPad application for viewing and manipulating 3D chemical and molecular
structures. Structures can be downloaded and displayed from the PubChem, PDB, and NCBI structure
databases together with the sequences for proteins and nucleic acids. Structures can be drawn as
tubes, ball and stick, or space filling modes. Coloring options include residue, charge, hydrophobicity,
rainbow, and molecule. Parts of structures can be hidden or displayed with mixed coloring and drawing modes.
Molecule World for iPhone
Molecule World for iPhone can be used on the iPhone or iPod touch to display and manipulate 3D chemical
and molecular structures from the PubChem, PDB, or NCBI structure databases. Drawing options include ball
and stick, space fill, and ball and stick modes. Coloring options include rainbow, residue, charge,
hydrophobicity, and molecule. Proteins, nucleic acids, and heterogens can be displayed in different modes.
Molecule World DNA Binding Lab
A classroom ready iPad application for exploring the ways chemicals and proteins bind to DNA.
The DNA Binding Lab uses Molecule World?s rendering engine and display features to highlight
different molecules and understand how they intact. The DNA Binding Lab includes instructions,
three examples, and 40 unknowns that can be assigned to students. Photo sharing capabilities allow
students to share their work with teachers to aid with assessment.
An iPhone application for PDB structures
A program for displaying
structures in both detailed and schematic formats and writing
images in various formats for Unix
Free, interactive visualization tutorials
Molecular Visualization Program and GUI of ZMM. MVM is a free
molecular viewer that can be used to display protein, nucleic
acids, oligosacharides, small and macromolecules. It has an
intuitive interface. In addition to being a molecular viewer, it
is the user interface of a very powerful molecular mechanics
PMV (Python Molecular Viewer)
An interactive molecular visualization and modeling environment
for manipulation and viewing of multiple molecules.
Program to view and manipulate PDB files on a PocketPC
Protein structure annotation using sequence profiles
Versatile annotation and high quality visualization of macromolecular structures
Analysis and visualization of macromolecular motions
Free viewer to display and manipulate PDB files and create animations
and slides of proteins for Windows. Online ordering of protein 3D prints
in several color schemes.
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. Supports Windows, Mac OSX, Unix, and Linux
An open source (GPL), interactive, high quality molecular
visualization system. QuteMol exploits the current GPU capabilites
through OpenGL shaders to offers an array of innovative visual
A free viewing system for PDB
coordinate files that runs on Mac (PPC), Windows, Unix, and Linux
Open source versions are also available.
A set of tools for generating
high quality raster images of proteins or other molecules.
Freeware for Mac OSX, Windows, Unix, and Linux
RasTop (v. 2.0)
A free user-friendly graphical interface to RasMol molecular
visualization software (v. 184.108.40.206), available for Windows and
A program for molecular
illustration and error analysis, for for Mac OSX, Windows, Unix,
RCSB MBT Viewers
The MBT toolkit is a framework that allows to create various viewers. It is used for 4 different viewers on the RCSB PDB web site.
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 for Mac (OSX or
PPC), Windows, or Unix
Schrödinger Product Suites
Schrödinger's full product offerings range from general molecular modeling programs
to a comprehensive suite of drug design software, as well as a
state-of-the-art suite for materials research. All products are run with
Maestro, a unified interface for all Schrödinger software, which is
available for Mac, Windows, and Linux.
The Structural Proteomics Application Development Environment (SPADE) provides
community tools for development and deployment of essential structure and
sequence equipment. Includes a chemical probing suite to support
experimental verification of predicted structural models. Written in Python
with scripting tools available. Runs on Windows, Linux and Mac.
Align proteins by sequence and 3D structure.
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. The software is available for Mac (OSX or PPC),
Windows, Linux, or SGI
A free and open-source tool with PDB format visualization
support written in fast memory efficient C++ code. Supports
Windows, Mac OSX, Unix, and Linux.
VMD (Visual Molecular Dynamics)
runs on many platforms including MacOS X, and several versions of
Unix and Windows. VMD provides visualization, analysis, and
Tcl/Python scripting features, and has recently added sequence
browsing and volumetric rendering features. VMD is distributed
free of charge.
A complete molecular graphics and modeling program, including interactive molecular dynamics simulations, structure determination,
analysis and prediction, docking, movies and eLearning for Windows, Linux and MacOSX.
A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics. Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral angles can be generated and exported. PDB files can be automatically downloaded from the RSCB PDB.