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.


CONTACT
David Johnson
emaildkjohnson@ku.edu
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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