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Deep sequence-structure-function learning for modeling and characterization of biomolecules at scale

Award Number: R35GM138146
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: 09/15/2020
PERIOD OF PERFORMANCE END DATE: 02/28/2031

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Deep sequence-structure-function learning for modeling and characterization of biomolecules at scale - PROJECT SUMMARY/ABSTRACT: The broad goal of the proposed research is to develop, evaluate, and disseminate a new generation of integrative deep sequence-structure-function learning methods and resources for modeling and characterization of biomolecules at scale. These advanced computational models can give insights into how biomolecules work, how they evolved, how they can be modulated, and how similar functions can be designed. My lab has been at the forefront of developing novel computational and data-driven methods, software, and information systems for diverse biological and medical problems, ranking among the best methods in community-wide blind assessments and serving the worldwide community of biomedical users. During the current project period, we have made substantial progress in addressing some of the urgent challenges and needs for developing new computational methods and resources for modeling biomolecular structures and interactions. This MIRA project has produced 20 publications covering research topics ranging from protein structure prediction and refinement, protein-protein and protein-nucleic acid interactions, as well as confidence estimation of predicted protein and nucleic acid structures. In addition, it also publicly disseminated eleven open-source software tools, two open-access webservers, and two freely available benchmark datasets to the community. Rigorous experimental validations of our methods in large-scale benchmarking as well as blind evaluations in community-wide CASP (Critical Assessment of Structure Prediction) challenges have demonstrated their feasibility and effectiveness. Building upon this demonstrated track record and ongoing momentum of scientific productivity, coupled with strong computing support and collaborative alliances, this renewal aims to continue and further expand this NIGMS-supported research program through the development of innovative, integrative, and scalable deep learning models for addressing some of the key challenges in structural biology by maximizing the accuracy, precision, coverage, and efficiency of structural characterization of biomolecules and their assemblies. Biology-guided, biophysics-informed, and experiment- assisted deep learning methods will be developed to complement and enhance existing approaches, aiming to deepen our understanding of the fundamental biomolecular sequence-structure-function relationship through the lens of computational modeling. Connections to experiments will be made via collaboration. The computational models proposed in this project are informed by and will shape the experimental hypotheses, promoting clinical feedback loops. The results from the project will lead to new computational methods and resources for understanding the molecular basis of complex diseases with important implications in drug discovery and human health.


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: 2026 ( Subtotal = $419,741 )
2026	2026	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	001	7	2/16/2026	COMPETING CONTINUATION	$419,741
2026	2024	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	000	6	2/16/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $419,741

Issue Date FY: 2024 ( Subtotal = $624,501 )
2024	2024	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	001	6	7/5/2024	NON-COMPETING CONTINUATION	$383,992
2024	2024	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	000	5	6/4/2024	SUPPLEMENT FOR EXPANSION	$240,509
														Subtotal = $624,501

Issue Date FY: 2023 ( Subtotal = $135,209 )
2023	2023	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	002	5	7/11/2023	NON-COMPETING CONTINUATION	$384,460
2023	2021	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	001	3	5/11/2023	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$1
2023	2021	AUBURN UNIVERSITY	321-A INGRAM HALL	AUBURN	AL	36849	LEE	USA	Biomedical Research and Research Training	000	2	5/4/2023	NON-COMPETING CONTINUATION	-$249,252
														Subtotal = $135,209

Issue Date FY: 2022 ( Subtotal = $383,454 )
2022	2022	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	002	4	9/20/2022	NON-COMPETING CONTINUATION	$376,518
2022	2021	AUBURN UNIVERSITY	107 SAMFORD HALL	AUBURN	AL	36849	LEE	USA	Biomedical Research and Research Training	000	2	9/2/2022	NON-COMPETING CONTINUATION	-$373,529
2022	2021	VIRGINIA POLYTECHNIC INSTITUTE & STATE UNIVERSITY	300 TURNER ST NW	BLACKSBURG	VA	24060	MONTGOMERY	USA	Biomedical Research and Research Training	001	3	9/6/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$380,465
														Subtotal = $383,454

Issue Date FY: 2021 ( Subtotal = $373,529 )
2021	2021	AUBURN UNIVERSITY	107 SAMFORD HALL	AUBURN	AL	36849	LEE	USA	Biomedical Research and Research Training	000	2	7/26/2021	NON-COMPETING CONTINUATION	$373,529
														Subtotal = $373,529

Issue Date FY: 2020 ( Subtotal = $362,119 )
2020	2020	AUBURN UNIVERSITY	107 SAMFORD HALL	AUBURN	AL	36849	LEE	USA	Biomedical Research and Research Training	000	1	9/11/2020	NEW	$362,119
														Subtotal = $362,119

Grand Total All Awards = $2,298,553

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Deep sequence-structure-function learning for modeling and characterization of biomolecules at scale

Award Number: R35GM138146

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: 09/15/2020

PERIOD OF PERFORMANCE END DATE: 02/28/2031

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