Center for Molecular Innovation and Drug Discovery

Design. Create. Innovate.

CHEMINFORMATICS & MOLECULAR MODELING

Molecular Modeling, Screening, and Visualization Resources

The Center’s primary computation hardware is a Linux-based multi-node cluster, which is powered by four NVIDIA Tesla K40 GPU accelerators. These accelerators have over 10,000 Cuda cores for parallel computing that increases performance over a regular cluster system by 40%. This system profoundly accelerates energy minimization, principal component analysis, and small molecule docking, allowing for the virtual high-throughput docking of 10 million drug-like compounds in only eight to ten hours.

In addition to the cluster, the Center houses multiple Linux-based workstations with NVIDIA Quadro Fx 5800 graphic cards, enabling the 3D visualization of macromolecules and evaluation of molecular modeling work. In-depth and powerful analysis of modeling results are viewed on CMIDD’s 3D visualization workstations. 

Our services include:

  • High throughput virtual screening of diverse libraries for novel therapeutic targets
  • Structure-based pharmacophore design, 3D-4D and higher order
  • QSAR model building
  • Scaffold hopping and de novo design
  • Construction of protein homology models and 3-D analysis
  • High level quantum mechanical computations of small molecules     
  • State-of-the-art software from Schrödinger, Tripos and Accelrys with parallel processing LINUX-based workstations

*Funding for the GPU Research Cluster was made possible by an Office for Research Equipment Grant.

Cheminformatics Instrumentation
Super Micro 6018R-TDW 1U Super Server Cluster with 4 Nodes, powered by Nvidia K40 Tesla GPU Three Linux-based workstations equipped with NVIDIA parallel core graphics processors, including 28 total processors and 580 CUDA cores
Schrödinger full suite molecular modeling software Accelrys DiscoveryStudio software
3D visualization monitor and glasses kit Tripos Sybyl-X software

Acknowledgements

The use of data generated in ChemCore in a grant application, progress report or publication contains the implicit understanding that the PI or authors will acknowledge the use of our facility. Acknowledgment of our core helps us demonstrate the impact we contribute to the research community, and it helps tremendously in our future effort to secure funding. Facility users should acknowledge ChemCore by including the following statement:

Molecular modeling and computational work was done by ChemCore at the Center for Molecular Innovation and Drug Discovery. ChemCore used resources supported by a Lever award from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust.

 


For cheminformatics and molecular modeling inquiries, please contact:
Rama Mishra, PhD | [email protected] | (847) 491-5335