Cukmody: (MD program for Proteins developed by R.I. Cukier, http://www.cem.msu.edu/~cukier/ )

Cukmody does Molecular Dynamics (MD) simulations on proteins, cofactors and solvent for fairly large systems. Used for mechanistic studies of enzyme catalysis, and studies of proton transfer and translocation in proteins.

SLIDE: (Developed by P.C. Sanschagrin, M.I. Zavodszky, and L.A. Kuhn, available for licensing to academic
and commercial researchers at http://www.bch.msu.edu/labs/kuhn/web/software.html )

SLIDE (Screening for Ligands by Induced-fit Docking, Efficiently) uses multi-stage indexing to identify drug binding sites in proteins. SLIDE can screen 100,000 compounds within 1-2 days. (Shown: estrogen in the binding-site of the human estrogn receptor.)

EST Library Browser: (Developed by M.D. Larson, R.G. Halgren, and C. Wilkerson, http://genomics.msu.edu)

The library browser allows one to conduct digital northerns to examine changes in gene expression between different tissues or following specific treatments. ESTs obtained from various cDNA libraries are grouped according to gene function. The relative expression of each EST is then graphically displayed according to library origin and functional category.

BLAST Report: (Developed by R.G.Halgren, M.D. Larson, and C. Wilkerson, http://genomics.msu.edu )

Part of our EST analysis pipeline, the BLAST Report toll reduces several hundred page Blast reports to several page summaries in an Excell or HTML (Web) format that include external links to the complete blast records and to genes with the most significant similarity matches.