Software Support

Glactone serves as a resource for chemical and biochemical software in the State of Georgia. Each year, workshops are run for specific software packages. Some software packages, faculty and staff can come to your institution and give an on-site tutorial to either the faculty or the students. Finally, the Glactone faculty and staff can answer email and phone requests from faculty at the institutions in Georgia.

Title: PCMODEL: Supplier: Serena Software
Platform: Windows, Linux and Mac
Function: Molecular modeling of organic and inorganic structures
Ease of Use: Freshman - senior
Description: PCMODEL allows students to make molecular models of organic and inorganic structures. It is an excellent program for visualizing structures and asking "what if?" questions on conformation analysis. It calculates heats of formation (very useful). It is a very cost-effective program in that relatively inexpensive site-licenses are available. Glactone has two series of exercises available for organic chemistry that can be freely copied and used.
Help Available: Substantial telephone and E-mail help are available; contact Don Harden or Dabney Dixon. You may also arrange for Drs. Harden or Dixon to visit your campus for a 3-hour tutorial that can be given to either faculty or students. Yearly week-long intensive tutorials for faculty are available through the Center for Workshops in the Chemical Sciences.
Title: Rasmol and freinds: Supplier: Molecular Visualization Freeware
Platform: Windows, Linux, UNIX and Mac
Function: Visualization of bimolecular structures
Ease of Use: Any level, but of substantial use for biochemistry
Description: This is an excellent program that can be used to visualize protein and DNA structures. It is exceptionally easy to use. It is free and in the public domain; students may download it to their computers. Protein and DNA structures are downloaded off the Internet from the Protein Data Bank. Most of the proteins discussed in Biochemistry I/II are on the Glactone web site.
Help Available: Substantial telephone and E-mail help are available; contact Don Harden or Dabney Dixon. You may also arrange for Drs. Harden or Dixon to visit your campus for a 3-hour tutorial that can be given to either faculty or students.
Title: Mage and friends: Supplier: The Richardsons' 3D Protein Structure Laboratory
Function: Visualize biomolecules
Platform: Windows, Linux, UNIX and Mac
Ease of Use: Elementary school - seniors
Description: Public domain program (available freely on the web) to visualize biomolecules. An outstanding program for teaching purposes. The six Protour files give one an overview. Other files can be downloaded off the web. Upper elementary school children seem to enjoy the colors and structures. College students like the text that accompanies the pictures. Note that each biomolecule in the database has been added by an individual, so there is a lack of uniformity.
Help Available: Telephone and E-mail help are available; contact Don Harden or Dabney Dixon.
Title: Protein Data Bank: Supplier: Research Collaboratory for Structural Bioinformatics
Function: X-ray and NMR structures of biological molecules
Platform: The World Wide Web
Ease of Use: Advanced undergraduates/faculty
Description: This database is the repository of all x-ray and NMR structures of biological molecules. Protein structures can be visualized directly in Rasmol. They can also be downloaded for input into other programs.
Help Available: Telephone and E-mail help are available; contact contact Don Harden or Dabney Dixon.
Title: SYBYL: Supplier: Tripos, Inc.
Function: Molecular Modeling of Biomolecules and ligand-bimolecular interactions
Ease of Use: Faculty or undergraduate research
Platform: Linux and UNIX workstations
Description: The SYBYL software package will preform Molecular Modeling, Mechanics, and Dynamics calculations on organic compounds and biomolecules. It is most useful in 3-dimensional structure elucidation of ligand-bimolecular interactions, such as a potential anti-cancer drug intercalating into a target segment of DNA. SYBYL is for those who wish to do drug design as an on going long term project.
Drawbacks: SYBYL, although very powerful, has a steep learning curve.
Help Available: Telephone and E-mail help are available; contact Don Harden or Dabney Dixon.
Title: SPARTAN: Supplier: Wavefunction
Platform: Windows, Linux, UNIX and Mac
Ease of Use: Junior, senior, faculty
Description: Spartan is a software package which will preform a variety of calculations on organic, inorganic, and organometallic molecules. These calculations include molecular mechanics,(SYBYL, MM2, and MM3 forcefields), semi-empirical molecular orbital calculations (MNDO, MNDO/d, AM1, and PM3), and ab initio calculations(Hartree-Fock, and PM2).
Drawbacks: Calculations may take a while with the PC version
Help Available: Telephone and E-mail help are available; contact Don Harden or Dabney Dixon. Also many of the colleges use this extensively and can provide help.