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    Science > Biology > Biochemistry and Molecular Biology > Biomolecules > Proteins and Enzymes > Structure  (43)

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  http://pymol.sourceforge.net/ http://pymol.sourceforge.net/
A free and flexible molecular graphics and modelling package which can be also used to generate animated sequences.
  http://www.ks.uiuc.edu/Research/vmd/ http://www.ks.uiuc.edu/Research/vmd/
A free program for visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies.
  http://jmol.sourceforge.net/ http://jmol.sourceforge.net/
Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
  http://www.umass.edu/microbio/rasmol/ http://www.umass.edu/microbio/rasmol/
Molecular visualization freeware for proteins, DNA, and macromolecules. Freely available for Windows, Macintosh, and UNIX.
  OpenRasMol http://www.openrasmol.org/
Provided for the convenience of users and software developers of open source versions of RasMol.
  Swiss-PdbViewer http://www.expasy.org/spdbv/
A free program for viewing and analyzing several proteins at the same time. Some energy minimzation and homology modeling features are also included.
  http://www.cmbi.ru.nl/~schaft/molden/molden.html http://www.cmbi.ru.nl/~schaft/molden/molden.html
Pre- and post-processing program for molecular and electronic structure, with Z-matrix editor, electron density visualization, and molecule animations. Available for Unix and VMS; free for academic use.
  UCSF Chimera http://www.cgl.ucsf.edu/chimera/
Highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus. Free of charge for academic, government, non-profit, and personal use.
  http://honiglab.cpmc.columbia.edu/grasp/ http://honiglab.cpmc.columbia.edu/grasp/
A visualization and analysis program useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. Commercial software.
  PyMolWiki http://www.pymolwiki.org/
User-contributed wiki to supplement the PyMOL documentation.
  gOpenMol http://www.csc.fi/gopenmol/
A free program for the analysis of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials. Supports many file formats like the GaussianXX, Jaguar, CHARMM, and AMBER.
  http://www1.bbiq.jp/zzzfelis/Facio.html http://www1.bbiq.jp/zzzfelis/Facio.html
3D-Molecular Modeling Software, available at no charge for the Windows platform. Has functions for visualization of biomolecules and results from GAMESS QM calculations, and for aligning and modifying structures.
  ChemCraft http://www.chemcraftprog.com
Windows-based program for visualization of molecular structures, vibrational modes, molecular orbitals, energy gradient and other properties from log files produced by the GAMESS and Gaussian packages.
  http://www.chemicalgraphics.com/PovChem/ http://www.chemicalgraphics.com/PovChem/
A chemical visualization and illustration program. Reads PDB files and exports POV-Ray files for producing high-resolution ray-traced images. Available for Windows, Linux, Mac, and SGI.
  Avogadro http://avogadro.openmolecules.net/
Open source advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers flexible rendering and a powerful plugin architecture.
  Jamberoo: Cross Platform Molecular Editor http://sf.anu.edu.au/%7evvv900/cct/appl/jmoleditor/index.html
Free cross-platform application for displaying, analyzing, editing, converting and animating molecular systems.
  http://viewmol.sourceforge.net/ http://viewmol.sourceforge.net/
An open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac. Available for Linux, FreeBSD, Mac OS X, and other Unices.
  Nanotube Modeler http://jcrystal.com/products/wincnt/
A program for generating and visualizing the xyz-coordinates for nanotubes, nanocones, nanosheets, and fullerenes. For Windows; free demo version available.
  Molcular Model Kits http://www.hgs-model.com/
Plastic molecular structure models for research and education in science, intended especially for biochemistry.
  http://www.teoroo.mkem.uu.se/daniels/ymol.html http://www.teoroo.mkem.uu.se/daniels/ymol.html
A free molecular visualization and animation program for the X window system. Creates images and movies, using either the built in renderer or povray. Still alpha.
  Historical Molecular Graphics http://www.umass.edu/molvis/francoeur/movgallery/moviegallery.html
Digitized versions of 16mm movies of molecular structures produced in the early days of interactive molecular graphics.
  Molegro Molecular Viewer http://www.molegro.com/mmv-product.php
A free cross-platform application for visualization and analysis of molecules and molecular docking results.
  ProteinScope http://www.proteinscope.com
ProteinScope is a free program to view and create animations of Protein Data Bank PDB files.
  Biodesigner and iMol http://www.pirx.com/
A molecular viewer for Windows9x systems with sequence editor and protein builder. Free for academic use. Additionaly the iMol molecule viewer is available for Mac OS X systems.
  http://cuemol.sourceforge.jp/en/ http://cuemol.sourceforge.jp/en/
Free molecular structure visualization and rendering program for Windows.
  SweetMollyGrace http://rodomontano.altervista.org/engSweetMG.php
A suite of freeware tools for automating work of rendering and animating molecules. Generates high quality images of molecules from PDB, XYZ, or molfiles using raytracing tools (Povray and Raster3D).
  OpenScience http://www.openscience.org/links.php?section=56
A directory of links to free molecule viewers and editors.
  http://www.polyhedron.co.uk/dtmm/dtmm.html http://www.polyhedron.co.uk/dtmm/dtmm.html
Desktop Molecular Modeller: A simple program for constructing and viewing small molecules and proteins in 3D with some energy calculation/minimization capabilities. Run on any PC with Windows 9X/NT. Commercial software.
  Molymod Molecular Models http://www.molecular-model.com/
Plastic molecular models for use in chemistry, biochemistry, molecular biology (DNA double helix), semiconductors and crystal lattice structures.
  http://www.geocities.com/thomas_r_bonner/vis/vis.htm http://www.geocities.com/thomas_r_bonner/vis/vis.htm
Molecular visualization software specialized for generating animations from molecular dynamics simulations.
  Review of Molecular Modelling Programs http://www.marcsaric.de/
Reviews, screenshots, and table of features comparing over a dozen freely available molecular modelling and viewing programs.
  http://www.labquip.clara.net/index.html http://www.labquip.clara.net/index.html
Plastic molecular models for constructing polypeptides and DNA molecules.
  http://hugin.ethz.ch/wuthrich/software/molmol/index.html http://hugin.ethz.ch/wuthrich/software/molmol/index.html
A free program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with emphasis on structures determined by NMR. Runs on UNIX and Windows NT/95. The site offers an online tutorial.
  Protein Explorer http://www.umass.edu/microbio/chime/pe/protexpl/
A web-based viewer for the 3D structures of proteins, DNA and RNA. Requires Netscape and the Chime plugin, which is only available for Windows9x.
  Santorini and Patmos, Molecular Viewer and Screensaver http://oeffner.net/development/
Read XYZ or PDB files of atoms and display them in a 3-dimensional view on Windows PCs.

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