The Computational Chemistry and Biology (CCB) Core Facility provides a wide array of advanced tools and services for computational-based simulations and modeling of chemical and biological systems. Located on the Anschutz Medical Campus of the University of Colorado in the new Skaggs School of Pharmacy and Pharmaceutical Sciences building, the CCB Core offers specialized expertise to researchers in both academia and the biotech/pharmaceutical industry to:
For a detailed summary of the equipment and services, the CCB Core provides, please click the specific links below or to the left.
Determining the structure and properties of a macromolecule, such as enzymes, antibodies, DNA, or RNA, is fundamental to understanding structure-activity relationships, protein-protein interactions, DNA/RNA binding, and small molecule design. The CCB Core utilizes validated scientific tools to aid in every step of macromolecule research. Services include:
The CCB Core can perform sophisticated simulations of the potential interactions between macromolecules, ligands, cofactors, membrane surfaces, and metal ions using advanced molecular mechanics, quantum mechanics, spatial alignments, and energetic calculations. Capabilities include:
A major goal of the CCB Core is to aid in the discovery and design of novel small molecule drugs by rapidly identifying and refining promising compounds utilizing a variety of strategies, including:
The CCB Core can perform early assessment of novel drug candidates by calculating predicted absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties for collections of molecules. The calculated results can be used to eliminate compounds with unfavorable ADMET characteristics and evaluate proposed structural alterations to improve ADMET properties prior to compound synthesis. The services include evaluation and prediction of:
The visualization of molecular structures and interactions is an essential aspect of analyzing and communicating the outcomes of modeling studies. Molecular graphics, sequence maps, 2D and 3D graphs, histograms, and heat maps are all viable methods to share the mechanistic insights resulting from computational analyses. The CCB Core specializes in the production of clear, concise, publication-quality graphics for grant submissions, manuscripts, reviews, and presentations. CCB Core personnel also have access to professional 3D modeling and animation software, such as Lightwave 3D, Cinema 4D, Modo, and Zbrush for the production of eye-catching figures, illustrations, animations, and cover art submissions that are not possible using traditional scientific modeling software.
Co-authorship of manuscripts for individuals involved in the modeling studies is generally expected as core personnel typically make significant contributions in the form of intellectual input, experimental design, data analysis/interpretation, and visualization of results. Core personnel will provide figures, figure legends, and manuscript text for the relevant methods, results, and discussion sections pertaining to the modeling studies. Authors should also be given the opportunity to review and edit the manuscript in its final form prior to submission.
In addition, acknowledgment of the CCB Core Facility should also be made in any publications that include data generated utilizing core facilities, resources, and/or software. An example of an appropriate acknowledgment would be: “The authors wish to thank the Computational Chemistry and Biology Core Facility at the University of Colorado Anschutz Medical Campus for their contributions to this manuscript.”
The CCB core is happy to provide letters of support, generation of preliminary results, and assistance in the writing of grant submissions. For letters of support, please allow at least 2 weeks from the time of your request for receipt of the letter. Please include the following information in your request: (1) title of the grant, (2) your title and mailing address, (3) agency to which you are submitting the grant and (4) 2-3 sentences on the specific aims and/or goals of the proposal.
For preliminary results and assistance in grant writing, please make your requests as soon as possible as preliminary studies typically have a turnaround of 4-6 weeks. However, more time may be required during periods of high utilization of the core facility (i.e. just prior to grant submission deadlines). Allocation of funds for computational studies and/or core personnel salary support in the grant budget qualifies the PI(s) for a flat rate to produce the necessary preliminary molecular modeling data (see Costs section below for further details). Obtaining grant support for longer-term CCB Core studies is a more cost-effective approach than utilizing the hourly fee-for-service rate structure, particularly if it includes salary support for core personnel.
The CCB Core offers training services for graduate students and postdocs in the use of the facility. A typical training session will last 1-2 hours and generally, 3-4 sessions are required to become proficient in the use of the software. Trained individuals have open access to one of four workstations, pending availability, and may submit jobs to the central server. This can reduce total costs for long-term studies by reducing the amount of time core personnel are required to spend on the project.
Fee-for-service prices are listed on a per hour basis, with the exception of the preliminary data rate. If the CCB Core Facility is specifically allocated funds in the proposal budget then all the costs associated with the generation of preliminary data, as well as assistance in writing of the proposal, are included in the single flat fee. The extent of the preliminary studies will be agreed upon in advance at the discretion of the CCB Core director. Fee for service estimates of total study costs can be made once the scope of the project is known.