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GLYCOPROTEIN MODELING SYSTEM FOR INTERNAL COORDINATE MECHANICS

Award Number: R43GM090418
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 04/01/2010
PERIOD OF PERFORMANCE END DATE: 03/31/2013

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GLYCOPROTEIN MODELING SYSTEM FOR INTERNAL COORDINATE MECHANICS - DESCRIPTION (provided by applicant): We propose to develop several essential components that would allow comprehensive modeling of glycoproteins in ICM: a carbohydrate extension of the ECEPP05 force-field, a library of common glycosylating moieties, tools for glycan construction on protein structures, and simulations of their stochastic dynamics and docking to glycan-binding proteins. Together these components will comprise the Glycosylation Modeling System. Carbohydrate moieties on the proteins (glycans) play an essential role in a range of physiological processes, including viral evasion from the immune system, blood anticoagulation, the progression of cancer, cell-cell recognition, and the correct folding and processing of proteins. Understanding of their function on the level of three-dimensional structure has been lagging behind that of the regular polypeptides. Flexibility, disorder and heterogeneity of glycans make experimental structure determination difficult. Molecular mechanics techniques increasingly allow in-silico simulation of essential biological processes at the atomic level. Molsoft's ICM (Internal Coordinate Mechanics) software platform is a particularly efficient modeling tool because of its use of internal variables, rather than traditional Cartesian coordinates, in the description of the molecular structure. This proposed development will allow to apply this approach to modeling of carbohydrates. Equipping structural biologists with the Glycoprotein Modeling System in ICM will help bring molecular simulations and structure predictions for glycans to the next level of accuracy. Successful structure modeling will ultimately help improve our understanding of molecular mechanisms underlying disease and help to accelerate structure-based drug discovery efforts. PUBLIC HEALTH RELEVANCE: Carbohydrate moieties on the proteins (glycans) play an essential role in a range of physiological processes, including viral evasion from the immune system, blood anticoagulation, the progression of cancer, cell-cell recognition, and the correct folding and processing of proteins. Equipping structural biologists with the Glycoprotein Modeling System in ICM will help bring molecular simulations and structure predictions for glycans to the next level of accuracy. Successful structure modeling will ultimately help improve our understanding of molecular mechanisms underlying disease and help accelerate structure-based drug discovery efforts.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2012 ( Subtotal = $0 )
2012	2011	MOLSOFT LLC	3366 N TORREY PINES CT #300	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	2	4/13/2012	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2011 ( Subtotal = $199,542 )
2011	2011	MOLSOFT LLC	3366 N TORREY PINES CT #300	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	2	3/14/2011	NON-COMPETING CONTINUATION	$199,542
														Subtotal = $199,542

Issue Date FY: 2010 ( Subtotal = $199,705 )
2010	2010	MOLSOFT LLC	3366 N TORREY PINES CT #300	LA JOLLA	CA	92037	SAN DIEGO	USA	Biomedical Research and Research Training	000	1	3/23/2010	NEW	$199,705
														Subtotal = $199,705

Grand Total All Awards = $399,247

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GLYCOPROTEIN MODELING SYSTEM FOR INTERNAL COORDINATE MECHANICS

Award Number: R43GM090418

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 04/01/2010

PERIOD OF PERFORMANCE END DATE: 03/31/2013

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