Featured Core Facility: Molecular Computation Core Facility (MCCF)

Computational techniques such as small molecule docking and molecular dynamics will be used in Kendal Ryter's lab (Dept. of Chem) to probe structure and function of Toll-like receptors (TLR) to aid in antagonist design. TLR models were obtained from Ilpo Vattulainen's lab at the Tampere University of Technology.

It is our pleasure to highlight the work arising from the CBSD’s Molecular Computational Core Facility (MCCF) in this July issue. During the last year, MCCF has been busy:

  • Using computational methods to determine structural interactions within the NMDA receptor ligand binding domain (LBD);
  • Collaborating on a project incorporating quantum calculations for ruthenium and hydride ions into the Generalized Amber Force Field for MD simulations;
  • And performing various docking studies to evaluate structure-activity relationships (SARs), to name just a few activities!

Over the past several years, MCCF expanded their capabilities, focusing on user-friendly software such as YASARA and powerful GPU-accelerated hardware. Software available through the MCCF includes modeling and simulation tools such as Amber 18, Gaussian 09, NAMD, SYBYL X, PyMol, and ChemDraw. Dr. Holley will deliver a seminar covering computational techniques on Oct. 4, 2019, in Skaggs 169 at 11 a.m.

Like other CBSD Facilities, the NIH-CoBRE primarily supports the MCCF with additional funding provided by UM’s Vice President of Research and Creative Scholarship (VPRCS). To enhance the sustainability of the Core, it has operated as a recharge facility with an established fee structure. UM faculty members who are unable to provide funding for their use of core facilities or need to acquire preliminary data leading to publications or grant applications are encouraged to consider applying for voucher funding. Staff and students from individual research laboratories are invited to consult with Dr. David Holley about how the MCCF resources can advance their research programs.

 

image caption:  Computational techniques such as small molecule docking and molecular dynamics will be used in Kendal Ryter's lab (Dept. of Chem) to probe structure and function of Toll-like receptors (TLR) to aid in antagonist design. TLR models were obtained from Ilpo Vattulainen's lab at the Tampere University of Technology.