CPFM Resources
The CPFM has as its scientific mission: the enabling the characterization of protein-ligand interactions in a broad (proteome-wide) manner using chemical probes. The purpose of such studies is to extract maximum value from recently available genomic information. To accomplish this goal, NMR, computational and related resources are being made available.
Computational tools include those for structure calculation, homology modeling (supplemented with NMR data), T1-based docking, ab initio docking into NMR-generated structures, etc.
Computational resources for such studies include SGI workstations and access to a Beowulf cluster. On-site software is available, such as DOCK, Autodock, Caveat, Grid and Modeller for docking and homology modeling, as well as DYANA for structure calculation, nmrPipe and XEASY for processing NMR spectra, as well as GRASP, VMS and MOLMOL for visualization. In addition to computational resources, any tools that may be of use in addressing the broader goal of characterizing protein-ligand interactions across protein families will be made available in the facility.
Since the development of such methods is a current focus at the CPFM, the facility is serving as a venue for dissemination of these new tools. For example, glassware and laser equipment needed to hyperpolarize 129Xenon (used in studying protein-ligand interactions) will be made available through the CPFM, as well as a custom-made probe insert for doing electrophoretic NMR. Under development are proteome-wide activity assays, NMR reagents for studying mechanism across protein families, fluorescent probes for imaging in zebrafish and generic broad-spectrum enzyme assays for high-throughput or in-gel screening. A chemoinformatics program is also being established that is powered by our recent acquisition of the PipelinePilot programming tools from SciTegic.
These and other Chemoinformatic tools will be used to create databases of drug building blocks, and potential endocrine disruptor pollutants - based on pharmacophore models. The centerpiece of the facility is the NMR spectrometer, and there are ongoing efforts to obtain a high-field NMR spectrometer for the facility as well.