SOLICITATION NOTICE
B -- CONFIGURATIONAL ENTROPY IN RECEPTOR-LIGAND BINDING; THE MIE-NN METHOD
- Notice Date
- 11/13/2009
- Notice Type
- Presolicitation
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Department of Health and Human Services, Centers for Disease Control and Prevention, Acquisition and Assistance Field Branch (Morgantown), 1095 Willowdale Road, Morgantown, West Virginia, 26505
- ZIP Code
- 26505
- Solicitation Number
- 000HCCCG-2010-77967
- Archive Date
- 12/30/2009
- Point of Contact
- Rebecca S Mullenax, Phone: 304-285-5880, Kimberly P Groves, Phone: 304-285-5885
- E-Mail Address
-
rmullenax@cdc.gov, kgroves@cdc.gov
(rmullenax@cdc.gov, kgroves@cdc.gov)
- Small Business Set-Aside
- N/A
- Description
- NOTICE OF INTENT TO ISSUE A PURCHASE ORDER. The Centers for Disease Control and Prevention (CDC), the National Institute for Occupational Safety and Health, NIOSH, Morgantown, WV, Health Effects Lab Division, Allergy and Clinical Immunology Branch in support of the Computational Biology Team requires professional services for the Configurational Entropy in Receptor-Ligand Binding: The MIE-NN Method. I. Background Modern biomedical research recognizes the critical role of computational studies in biology, molecular medicine, and toxicology. The goal of the Computational Biology Team is focused on the calculation of the thermodynamic concept of entropy for molecular systems involved in binding smaller ligands to receptors located on larger macromolecular systems. Specifically, the contribution of rotation about intramolecular bonds and the constraint of associated energetics of those bonds with binding of ligands is the focus of the Configurational Entropy Project. The mission of the Computational Biology Team is focused on modeling and quantitatively estimating entropy using the fundamental and well established theories of statistical mechanics. In collaboration with key investigators at the Center for Advanced Research in Biotechnology (CARB) at the University of Maryland Biotechnology Institute, the Team has successfully identified a tractable method to deal with the most challenging aspect of modeling the energetics of binding-the configurational entropy.1 It combines the theory of mutual information expansion (MIE) originally identified by CARB investigators2 with the non-parametric methods of nearest neighbor (NN) estimation of entropy identified by the Team.3 It is called the MIE-NN method. This appears to be a novel method with far reaching implications in the fields of chemical toxicity characterization and of drug design. Initial successes in simple molecular systems are being validated in more realistic systems, and expanded to include effects of solvation and ion binding. II. Project Objectives Related to this Contract 1. Implement software needed to estimate configurational entropy with the MIE-NN method, allowing for calculations in large systems with several hundred variables. Due to the sheer physical size of computer files used and the number of variables analyzed for such large systems (e.g. cyclodextrin and ER), an enormous burden is placed on computer resources to read and edit these files. It is necessary to develop software procedures to provide an accurate, efficient, and robust solution to this demand. The hardware and software systems must allow for several MIE calculations to be run concurrently and results of these calculations to subsequently undergo a process of concatenation/compilation to achieve final configurational entropy estimates. The computational system must allow ongoing calculations to be stopped and then restarted due to unexpected events (e.g. prolonged power failure, system updates that require rebooting, etc.) or software upgrades that provide significant increases in efficiency. All these factors may result in the output being significantly fragmented but salvageable. In order to avoid possible human error in the concatenation/compilation process, it must be highly automated to obtain final MIE NN based entropy estimations. Lastly, the software system underlying the MIE-NN method of configurational entropy estimation is ready to be incorporated into a computer platform publically available to computational physicists, chemists, and biologists. This is a major goal of this contract. 2. As a specific extension of previous collaborations with CARB, a protein structure that meets NIOSH mission needs has been identified. This addresses the need to develop the MIE-NN approach in a biologically natural receptor-ligand system. It is the estrogen receptor alpha (ER) protein. This system meets needs to have a computationally tractable model to elucidate important methodological issues still inherent to validating the MIE-NN approach; and it will contribute significantly to practical needs to estimate binding affinities for molecular systems with potential toxicities. The molecular dynamics simulation of positional and energetic states is currently in progress, and remains to be monitored and completed during the course of this contract. In addition, MIE-NN calculations for the dipyridyl/ethyleneurea model system are to be concluded. Responsible sources that believe they possess the expertise and capabilities identified above are encouraged to submit to the Contracting Officer within 15 days from the posting date of this notice, their written capabilities statement and pricing information in the format they choose, not to exceed 10 pages. Please forward the capability statement and pricing information to Rebecca Mullenax, Purchasing Agent, Reference 000HCCCG-2010-77967, CDC NIOSH, 1095 Willowdale Road, Morgantown, WV 26505, or e-mail to RMULLENAX@CDC.GOV or FAX to 304-285-6083. Phone 304-285-5880. All vendors must be registered in the Central Contractor Registry (CCR) prior to an award of a federal contract. The website is: www.ccr.gov. The Government will review any/all capabilities statements and pricing information submitted and determine if other qualified sources do exist that could provide this requirement. Information received in response to this announcement will be used solely for the purpose of determining whether to conduct a competitive procurement. If no affirmative responses are received within 15 days, in accordance with FAR 13.106-1(b)(1), negotiations will be conducted with the University of Maryland, Biotechnology Institute, 701 East Pratt Street, Suite 200, Baltimore, MD 21202-3101 as the only source and a purchase order will be issued without any additional notic
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