Featured Core Facility: Molecular Computation Core Facility (MCCF)

Our structure-based design strategy of a potential peptide agonist to the IL-1 Receptor 3 protein (IL-1R3) is guided in part through electrostatic complementarity surface maps generated by Flare software (cresset-group.com). The IL1-R3 surface is colored in degrees of red denoting electrostatic clashes between IL-1R3 and the bound peptide (green and brown ribbon cartoon), and degrees of teal denoting more harmonious electrostatic interactions between IL-1R3 and the peptide agonist.

Image caption: Our structure-based design strategy of a potential peptide agonist to the IL-1 Receptor 3 protein (IL-1R3) is guided in part through electrostatic complementarity surface maps generated by Flare software (cresset-group.com). The IL1-R3 surface is colored in degrees of red denoting electrostatic clashes between IL-1R3 and the bound peptide (green and brown ribbon cartoon), and degrees of teal denoting more harmonious electrostatic interactions between IL-1R3 and the peptide agonist.

The Molecular Computation Core Facility (MCCF), located in Skaggs 482, is a resource for the University of Montana students, staff, and faculty interested in learning and using computational chemistry tools. The MCCF director, Dr. Bowler, and manager, Dr. Holley, encourage both collaborative and independent research, with Dr. Holley on hand to help with strategy design and implementation, as well as to help with technical questions. Recently, Drs. Holley and Bowler have focused on enhancing the core’s usability by investing in graphical-based, user-friendly software, and hardware. These new investments should significantly decrease learning curves associated with older-school command line-oriented hardware and software, and hopefully make computational chemistry much more accessible. The purchase of two Macintosh iMac workstations, each installed with powerful, cutting-edge software platforms (e.g., YASARA, Spark, Flare, Forge) highlights our efforts to facilitate low-barrier entry to in silico studies. These platforms provide intuitive, graphical interfaces for molecular dynamics, small molecule docking, structure-based drug design, pharmacophore modeling, electrostatic mapping, and quantum mechanics calculations. For more details of what these tools can do for you, please contact Dave Holley (dave.holley@umontana.edu) or Bruce Bowler (bruce.bowler@umontana.edu), and they will get you started.