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Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug design

Award Number: R01GM132386
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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PROJECT SUMMARY/ABSTRACT Molecular simulation is a powerful tool to predict the properties of biomolecules, interpret biophysical experiments, and design small molecules or biomolecules with therapeutic utility. However, a number of obstacles have impeded the development of quantitative, cloud-scale research work¿ows involving biomolecular simulation. Two main ob- stacles are the insuf¿cient accuracy of current atomistic models for biomolecules and small molecule therapeutics and the lack of interoperability in simulation toolchains used in both academic and industrial biomolecular research. Our original R01, “Open Data-driven Infrastructure for Building Biomolecular Force Fields for Predictive Bio- physics and Drug Design,” seeks to solve the ¿rst problem. It helps fund our effort, the Open Force Field Initiative (https://openforce¿eld.org) to develop open, extensible, and shared software and data infrastructure, implementing statistically robust methods of parameterizing force ¿elds and choosing new force ¿elds in a statistically sound manner. This work is designed to create not just a new generation of force ¿elds, but an open technology to continue advancing force ¿eld science. However, even with improved molecular models, putting together complete work¿ows of biomolecular simulations involves interfacing substantial numbers of different tools. However the majority of the existing molecular simulation work¿ows are mutually incompatible, with differing representations of the molecular models. The Open Force Field Initiative effort already includes the development of molecular data structures that we can ex- port into existing molecular simulation tools. We propose to extend the existing scope of our R01 to create an extensible common molecular simulation representation and translators to and from this representation. Such a set of tools will immediately make it signi¿cantly easier to combine the disparate work¿ows developed for different sets of molecular simulation tools. Researchers will be able to set up and build the biophysical simulations using their usual tools, but run and analyze them with currently incompatible tools, enabling better matching of computational resources and methods to problems. It will help avoid trapping in a single software framework, and enable combinations of functionalities previously impossible without substantial developer time and effort. We will (Aim 1) work with partners to generalize our modular, extensible object model for representing parameterized biomolecular systems in a manner that accommodates the force ¿eld terms currently supported by most popular biomolecular simulation packages. We will engineer it to be extensible to advanced interaction forms, such as polarizability and other multibody terms, and machine learning models for intermolecular forces. We will (Aim 2): enable easy conversion between components of molecular simulation work¿ows by allowing other molecular simulation packages to easily store their representations in this data model, developing converters that can import/export this object model to multiple popular ¿le formats, focusing initially on OpenMM, AMBER, CHARMM, and GROMACS. We will demonstrate the utility of this interface in cloud-ready work¿ows.


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: 2023 ( Subtotal = $601,611 )
2023	2023	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	000	4	4/21/2023	NON-COMPETING CONTINUATION	$601,611
														Subtotal = $601,611

Issue Date FY: 2022 ( Subtotal = $731,709 )
2022	2022	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	002	3	7/11/2022	SUPPLEMENT FOR EXPANSION	$10,780
2022	2022	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	000	3	2/24/2022	NON-COMPETING CONTINUATION	$648,834
2022	2022	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	001	3	6/29/2022	NON-COMPETING CONTINUATION	$72,095
														Subtotal = $731,709

Issue Date FY: 2021 ( Subtotal = $786,542 )
2021	2021	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	004	2	4/9/2021	NON-COMPETING CONTINUATION	$0
2021	2021	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	000	2	2/18/2021	NON-COMPETING CONTINUATION	$608,856
2021	2021	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	005	2	8/30/2021	SUPPLEMENT FOR EXPANSION	$177,686
2021	2020	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	002	1	4/2/2021	SUPPLEMENT FOR EXPANSION	$0
2021	2020	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	001	1	4/2/2021	NEW	$0
2021	2020	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	003	1	4/2/2021	SUPPLEMENT FOR EXPANSION	$0
														Subtotal = $786,542

Issue Date FY: 2020 ( Subtotal = $996,568 )
2020	2020	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	002	1	9/1/2020	SUPPLEMENT FOR EXPANSION	$225,000
2020	2020	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	000	1	2/12/2020	NEW	$675,565
2020	2020	REGENTS OF THE UNIVERSITY OF COLORADO, THE	3100 MARINE ST STE 481 572 UCB	BOULDER	CO	80309	BOULDER	USA	Biomedical Research and Research Training	001	1	6/25/2020	SUPPLEMENT FOR EXPANSION	$96,003
														Subtotal = $996,568

Grand Total All Awards = $3,116,430

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Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug design

Award Number: R01GM132386

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

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