Parsing SDF files
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PowerMV (available for MS Windows at http://www.niss.org/PowerMV/ ) is probably the best
choice as it displays all structures and associated properties together in one screen. After
launching the program, click on the SDF icon on the toolbar and select the SDF file to be
loaded. A new compound field is created; double click on it to view the structures. Check
Show Attributes to see the associated data, such as antibacterial activity and the incidence of
adverse reactions.
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ACD/ChemSketch (available for MS Windows at
http://www.acdlabs.com/products/chem_dsn_lab/chemsketch ) is a nice structure editor that
accepts SDF files as one of its many input formats. However, you need to load the SDF-To-
Sketch converter via Options ... ChemBasic Organizer into the toolbar before you can load SDF
files. It is best to display one molecule per page from the SDF file; you can use PgUp and
PgDown keys to scroll trough the structures. I am not sure how to display the properties. An
interesting feature is the ability to search PubChem and eMolecules databases using molecular
structures as inputs; you can try to see if any of the 20 molecules are known drugs. The
program also performs 2D to 3D coordinate conversions and generates SMILES strings.
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MarvinView (trial version available upon request from
http://www.chemaxon.com/product/mview.html ) is Java based and thus should work for people
who do not have access to MS Windows platform. Please see their comprehensive
documentation on how to visualize SDF files.
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PyMOL (available at http://delsci.com/rel ) is a visualization and modeling program for MS
Windows, MacOS, and Linux. It places each structure in the SDF into own state/frame; you can
use the player functions to browse individual structures. I am not aware of an easy way to
display properties within PyMOL.
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UCSF Chimera (available at http://www.cgl.ucsf.edu/chimera ) is another multi-platform
visualization and modeling program. It places each structure in the SDF file into own model;
you can use the ModelPanel to select and move individual structures. You can move active
structures freely around; for example you can group similar structures into one are of the screen
and rotate them to emphasize the similarity.
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Mathematica 7 from Wolfram Research can import and
interactively visualize SDF files. For example, to generate 3D representation of chorismate mutase
inhibitors in the SDF virtual library, use
inhibitors = Import["http://www.chem.ucsb.edu/~kalju/chem162/private/cm_inhib.sdf", "Graphics3D"].
Note that this does not work with earlier versions of Mathematica.