MGM Lab Services

The Molecular Graphics and ModelingMolecular Graphics and Modeling Laboratory provides a number of computational services aimed toward chemical biology and translational science in biomedical research. For example:

  • Machine learning and data mining for large scale, multidimensional chemical biology data sets
  • Docking and virtual screening of small molecule ligands against protein targets of interest
  • Molecular dynamics simulation and modeling of small/macro molecules, proteins, and biomolecular systems
  • Analysis of structure-activity relationships
  • Visualization and graphics of biomolecules and biomolecular systems
  • Custom algorithm/software development along with databases and web applications

The laboratory houses and maintains servers, clusters, and workstations that facilitate compute, storage, database, and visualization applications among others. The laboratory provides a number of commercial and open-source software packages, including Schrodinger MacroModel Suite, Tripos SYBYL Suite, Cambridge Crystallographic Database, AutoDock and AutoDock Vina. Additionally, a number of supporting software tools are available such as AMBER, GAMESS, Gaussian 98, LAMMPS, EMBOSS, CHARMm, and PyMol. Additional drug design tools include additional docking utilities (FlexX, FlexE, Flex-Pharm, CScore), QSAR/CoMFA, VolSurf, and UNITY. The MGM Lab possesses a huge virtual chemical library collection (more than 15 million 3-D structures) including the ChemNavigator collection, the PubChem small molecules database, plus smaller Maybridge, NCI, ChemDiv, ChemBridge, IBS and LeadQuest libraries. MGM lab hardware includes a 20 processor Linux cluster, a 10 processor workstation / cluster hybrid, a 16 processor compute server, a database server, web server, application server, and storage server. Total disk storage capacity is on the order of 20 TB. The MGM lab also maintains an open lab/work space with several desktop workstations allowing students, staff, and faculty to use software tools and seek assistance.

David Johnson
Access to more than 40 computational chemistry software programs and databases
High-performance computational tools accelerate drug discovery and minimize costs
Analyze complex, multidimensional data sets to rapidly generate biological insights
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