The Crystallography and Computational Biosciences (CCB) Shared Resource serves as a portal for access to:
- State-of-the-art X-ray crystallographic equipment
- Technical support
- High-performance computing
- Scientific consultation for Cancer Center researchers
The CCB meets the growing needs for structure determination and computational analysis of protein and DNA/RNA structure, function and dynamics for a diverse array of projects ranging from basic science questions to drug design.
The Crystallography and Computational Biosciences Core supports areas of basic science research with an emphasis on biological processes related to cancer such as:
- Cell signaling
- Transcriptional regulation
- DNA damage and repair
- Lipid metabolism
We provide access to cutting-edge modeling and simulation methods. The information from these complementary approaches can be used to develop novel therapies, as it’s essential for assessing and exploiting the biological function of the target protein.
The CCB also provides support for ongoing projects and the development of new projects through the collection of preliminary data for funding applications.
Capabilities and Expertise
Our structural biology team has expertise in macromolecular crystallography and works with investigators on all levels of structure determination.
Some examples of recent collaborations include:
- Development of PI3K-kinase inhibitors
- Development of fatty acid synthase inhibitors
- Dissection of the molecular basis for peroxiredoxin inactivation and repair by sulfiredoxin
- Structure and function of the mammalian TREX1 3' exonuclease and RNase H2 enzymes
Services We Provide
Our computational biology expertise lies in structure-based classical modeling, docking, and analysis, but we also have expertise in computational biology/bioinformatics, and in quantum mechanical calculations.
Macromolecular X-ray crystallography is an experimental method to determine the three-dimensional structure of proteins, DNA/RNA, their complexes and the complexes of a variety of ligands including cofactors, substrates, drug candidates, etc.
- Consulting on all aspects of protein expression, purification and feasibility of structure determination
- Identification of crystallization conditions and possible other existing structures
- Access to X-ray diffraction facility
- Determination of the molecular structure through collaboration
- Determine if the problem is amenable to computation.
- Decide what sort of computations need to be performed.
- Determine if the scale of the computations involved are worth the time.
Calculations that can be readily performed:
- Molecular dynamics
- Protein-protein docking
- Protein-ligand docking
- Various bioinformatic analyses
- Reaction-diffusion modeling, quantum mechanical calculations and other mathematical modeling may be possible
- Gryphon 96 well crystallization robot (Art Robins Instruments)
- Crystallization cabinets
- Several multi-processor graphics workstations with hardware stereo for model building and refinement
- Linux cluster with the appropriate software for computational calculations such as molecular dynamics in silico drug docking and homology modeling
- Intensive calculations and molecular dynamics simulations through access to the DEAC computing cluster and GPU workstations
- Rigaku Micromax 007 X-ray source with dual VariMax-HF Confocal Optic Systems coupled to Pilatus 3R and RAXIS4+ detectors