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Delphi and associated resources: maintenance and further development; Administrative Supplements to Support Undergraduate Summer Research Experiences

Award Number: R01GM093937
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: 08/10/2010
PERIOD OF PERFORMANCE END DATE: 02/29/2024

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Delphi and associated resources: maintenance and further development; Administrative Supplements to Support Undergraduate Summer Research Experiences - Modeling macromolecular thermodynamic properties, such as stability, dynamics and interactions, is essential for revealing details of biochemical processes occurring in the cell and further for figuring out what molecular effects are causing diseases. Among the forces and energies manifested at atomic level of details, the electrostatics is one of the most prominent, because all atoms carry partial charge and the electrostatic force is a long-range force dominating all other forces at long distances. Particularly, the electrostatics is the driving force for pH- dependence of macromolecular stability and activity. However, modeling electrostatic forces and energies of biological macromolecules is highly nontrivial because of their irregular shape, the conformational changes occurring during the corresponding process and the presence of water phase. An efficient way to overcome such a complexity is to consider water phase and macromolecule(s) on the same footage as continuum media with inhomogeneous polarizability. This is the approach currently available ONLY in DelPhi package, where internal cavities, low density macromolecular regions and surface waters are modeled via inhomogeneous Gaussian and super-Gaussian dielectric functions. In a series of works, it has been shown that this approach outperforms the traditional two-dielectric model and delivers ensemble-averaged quantities. With this proposal we are seeking support to continue maintaining and developing DelPhi suite and associated resources. In parallel with continuous support that we provide to our users (more than 7,000 registered users), we plan to develop many new features in DelPhi as: (1) enabling DelPhi to handle molecular dynamics (MD) generated trajectories by the most frequently used MD packages as NAMD, CHARMM, GROMACS and AMBER; (2) upgrading DelPhi to model geometrical properties as volume and molecular surface, which combined with (1) will allow DelPhi to carry MM/PBSA calculations without third party software in fast and efficient manner; (3) estimation of entropy, (4) novel energy partitioning and (5) residue-specific Gaussian-based dielectric function. These new developments will be used to improve and completely re-design DelPhi associated resources as SAAFEC, SAAMBE, and SAMPDI, which are methods for predicting the change of the protein folding, protein binding, and protein-RNA/DNA binding free energies due to mutations, respectively. In parallel, machine learning (ML) approaches will be utilized to improve SAAFEC, SAAMBE and SAMPDI performance and a new feature “Gaussian total density” will be implemented in the ML protocols.


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: 2024 ( Subtotal = -$36,468 )
2024	2023	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	001	11	8/27/2024	NON-COMPETING CONTINUATION	-$35,881
2024	2023	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	11	1/25/2024	NON-COMPETING CONTINUATION	$0
2024	2023	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	002	11	8/27/2024	SUPPLEMENT FOR EXPANSION	-$587
														Subtotal = -$36,468

Issue Date FY: 2023 ( Subtotal = $371,023 )
2023	2023	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	11	2/15/2023	NON-COMPETING CONTINUATION	$365,050
2023	2023	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	001	11	5/24/2023	SUPPLEMENT FOR EXPANSION	$5,973
														Subtotal = $371,023

Issue Date FY: 2022 ( Subtotal = $375,603 )
2022	2022	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	002	10	8/3/2022	COMPETING CONTINUATION	$9,866
2022	2022	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	10	3/25/2022	COMPETING CONTINUATION	$375,603
2022	2019	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	001	9	8/3/2022	NON-COMPETING CONTINUATION	-$9,866
														Subtotal = $375,603

Issue Date FY: 2021 ( Subtotal = $0 )
2021	2019	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	9	2/23/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2019 ( Subtotal = $362,798 )
2019	2019	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	9	2/15/2019	NON-COMPETING CONTINUATION	$362,798
														Subtotal = $362,798

Issue Date FY: 2018 ( Subtotal = $363,101 )
2018	2018	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	8	2/27/2018	NON-COMPETING CONTINUATION	$326,790
2018	2018	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	001	8	5/7/2018	NON-COMPETING CONTINUATION	$36,311
														Subtotal = $363,101

Issue Date FY: 2017 ( Subtotal = $363,377 )
2017	2017	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	003	7	6/2/2017	NON-COMPETING CONTINUATION	$36,338
2017	2017	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	002	7	2/15/2017	NON-COMPETING CONTINUATION	$327,039
2017	2016	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	001	6	10/26/2016	COMPETING CONTINUATION	$55,560
2017	2014	CLEMSON UNIVERSITY	201 SIKES HALL	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	5	10/26/2016	NON-COMPETING CONTINUATION	-$55,560
														Subtotal = $363,377

Issue Date FY: 2016 ( Subtotal = $363,629 )
2016	2016	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	001	6	5/13/2016	COMPETING CONTINUATION	$363,629
2016	2014	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	296345355	PICKENS	USA	Biomedical Research and Research Training	000	5	5/12/2016	NON-COMPETING CONTINUATION	$0
														Subtotal = $363,629

Issue Date FY: 2014 ( Subtotal = $371,078 )
2014	2014	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	5	7/16/2014	NON-COMPETING CONTINUATION	$371,078
														Subtotal = $371,078

Issue Date FY: 2013 ( Subtotal = $389,873 )
2013	2013	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	4	7/30/2013	NON-COMPETING CONTINUATION	$389,873
														Subtotal = $389,873

Issue Date FY: 2012 ( Subtotal = $437,203 )
2012	2012	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	3	8/1/2012	NON-COMPETING CONTINUATION	$437,203
														Subtotal = $437,203

Issue Date FY: 2011 ( Subtotal = $445,665 )
2011	2011	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	2	7/22/2011	NON-COMPETING CONTINUATION	$445,665
														Subtotal = $445,665

Issue Date FY: 2010 ( Subtotal = $420,605 )
2010	2010	CLEMSON UNIVERSITY	PO BOX 345355	CLEMSON	SC	29634	PICKENS	USA	Biomedical Research and Research Training	000	1	8/9/2010	NEW	$420,605
														Subtotal = $420,605

Grand Total All Awards = $4,227,487

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Delphi and associated resources: maintenance and further development; Administrative Supplements to Support Undergraduate Summer Research Experiences

Award Number: R01GM093937

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: 08/10/2010

PERIOD OF PERFORMANCE END DATE: 02/29/2024

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