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SGD Help: Protein Structure Viewers

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Description

To address questions we occasionally receive about the availability of protein structure viewers on various platforms, we created this protein viewer resource page. This page describes resources available for viewing three dimensional protein structures, either through a stand-alone program installed on your desktop or through a plug-in that works with your web browser. Much of this information is based on the resource page provided by the PDB; for a more extensive list of resources, go to their site.

Protein Structures in SGD

SGD provides structural information pertaining to yeast proteins via its PDB Homolog tool. You can reach this tool by choosing the PDB Homolog option from the Protein Info & Structure menu on the right side of SGD Locus Pages. You can also retrieve this information from the PDB Homolog Search Page.

All yeast proteins are compared using the Smith-Waterman algorithm to the sequences available in the PDB, and links are provided from the results page to the structures of the homologous sequences. Thus, if the structure of a particular yeast protein has not yet been solved, but the structure of a homolog in another species is available, this tool will provide the link to the homologous structure. The PDB Structure link on the results page goes to the View Structure page at PDB, which provides links to various protein viewers.

For more information on the PDB Homolog tool, see the PDB Homolog Help page at SGD.

Programs for Viewing Protein Structures

The following list of tools for viewing and analyzing protein structures is based on the one provided by PDB. Note that some of these may be commercial products that require a license. If we have missed an important resource, please let us know, and we will add it to the list.

Note for Safari users on Mac OS X: there seems to be a general problem with Safari when trying to use plug-ins/helper applications. Instead of launching the plug-in, Safari downloads the HTML page. Apple has been notified of this problem. Plug-ins listed below have been tested and work well using Netscape on Mac OS X as indicated.

Tool Type OS/Platform Notes
PyMOL stand alone Mac (OS X), Windows, Unix, Linux Powerful, scriptable viewer, optimized for Mac OS X; introduction and sample files are available.
NCBI Cn3D web browser plug-in Mac (PPC or OS X), Windows, Unix Very good tutorial available.
iMol stand alone Mac (OS X) Uses Open GL graphics, can perform many functions including superimposing structures.
VMD stand alone Mac (OS X), Windows, Unix Visualization tool, also can be used for analysis; scriptable.
MOLMOL stand alone Mac (OS X), Windows, Unix, Linux Emphasis on NMR structures.
PDB2MGIF web browser plug-in Mac (OS X), Windows, Unix, Linux Makes animated gifs of PDB files. Instructions are provided by PDB.
Raster3D stand alone Mac (OS X), Windows, Unix, Linux Produces high quality raster images of proteins.
Ribbons stand alone Mac (OS X), Windows, Unix, Linux Visualization and error analysis tool.
WebMol stand alone or applet Mac (OS X), Windows, Unix: applet; Windows, Unix: stand alone Displays and analyzes PDB records via the web.
canDo Shockwave 3D PDB Viewer web browser plug-in Mac (PPC or OS X), Windows Can view PDB files over the web.
Mage stand alone and Java web version Mac (PPC or OS X), Windows Reads Kinemage files, provides utility (Prekin) to convert PDB to kinemage
SwissPDB Viewer stand alone Mac (PPC or OS X), Windows, Linux, SGI Can use to analyze multiple models and to build models into electron density maps.
Rmscopll plug-in and command line Mac (PPC or OS X), Windows, Unix Redirects structure files or RasMol scripts to multiple RasMol sessions.
MolView and MolView Lite stand alone Mac (PPC) Can display various types (ribbon, stick, etc) of structure representations.
RasMol stand alone Mac (PPC), Windows, Unix, Linux Visualization tool for PDB files.
MolScript stand alone Unix Displays 3D structures in schematic or detailed representations; also produces several different types of output formats.
BioEditor stand alone Windows Can create and present structure annotations; requires MDL Chime.
MDL Chime web browser plug-in Windows Popular viewer that reads PDB files.
ProteinScope stand alone Windows Can display PDB files, create excel files from PDB records, and make animations and slides.
Qmol stand alone Windows Open GL viewer.
ViewerPro stand alone Windows From Accelrys; high-end commercial package.
RasTop stand alone Windows, Linux Graphical interface for RasMol.
Java3D Molecular Visualization stand alone Windows, Unix Open source freeware Java viewer, from adcworks.
POLYVIEW web-based Any platform that supports web browsing Protein structure visualization server that can be used to generate schematic representations of secondary structures, relative solvent accessibility, and physical-chemical property profiles. View examples and options.

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