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Development of a new TSR algorithm to represent sequences of proteins and 3D structures of nucleotides and molecular complexes for mechanistic understanding of protein sequence and structure relations

Award Number: R15GM144944
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: 09/15/2021
PERIOD OF PERFORMANCE END DATE: 05/31/2029

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Development of a new TSR algorithm to represent sequences of proteins and 3D structures of nucleotides and molecular complexes for mechanistic understanding of protein sequence and structure relations - Project Summary During the investigation of the current R15 project, we have learned that (i) a new method is needed for quantifying not only individual molecular structures, but also structures of molecular complexes for accelerating discovery and (ii) a new method for protein 1D sequence comparisons is needed for complementing the Triangular Spatial Relationship (TSR) algorithms for 3D structural comparisons. The TSR algorithms have been centered on individual molecules. However, the essence of life lies in the complex interplay and interactions between molecules, not single molecules themselves. Dataset preparation and annotation are needed for the use of the 3D TSR algorithms both of which require sequence analyses. Protein sequence analyses are also needed for interpreting the results from protein structure analyses. These discoveries have motivated us to develop the current proposal. The long-term goal is to understand protein sequence, structure and function relations. The rationale of this project is based on our previously published results primarily focused on individual molecules. The TSR algorithms have been demonstrated to be effective for quantifying the conformational changes, identifying interface structural characteristics, relating drug structures to their binding affinities, implementing a parallelization strategy for handling large datasets and complementing other computational methods. The scientific questions for which we can provide evidence include (i) Is there a code for molecular recognition? (ii) How does an amino acid sequence directly translate into the final 3D structure? The main objectives of this proposal are to develop novel computational methods and software tools for building direct links between protein sequences and structures for mechanistic understanding of protein sequence and structure relationships and for quantifying conformational changes for mechanistic understanding of molecular recognition. The central hypothesis is that protein 1D sequences and 3D structures can be divided into a set of the smallest unit: a triangle that can be represented by an integer (a TSR key) through a set of rule-based formulae. To achieve the objectives and contribute to answering the unresolved questions, we propose the following five specific Aims: Development of a new method for representing protein sequences using 1D TSRs for understanding protein sequence relationships and discovering sequence motifs (Aim 1); Understanding protein sequence and structure relationships using 1D and 3D TSR keys (Aim 2); Representing molecular fingerprints using 3D TSR keys (Aim 3); Development of a new method for representing nucleotide 3D structures and mechanistic understanding of DNA and transcription factor interactions (Aim 4); Integration of experimental and computational data for mechanistic understanding of protein and protein interactions (Aim 5). The representation methods of protein 1D sequences and molecular 3D structures are innovative and the proposed research will have significant impacts on research in the fields of structural biology and chemistry and accelerating drug development for pharmaceutical industries.


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 = $491,338 )
2026	2026	UNIVERSITY OF LOUISIANA AT LAFAYETTE	104 E UNIVERSITY AVE	LAFAYETTE	LA	70503	LAFAYETTE	USA	Biomedical Research and Research Training	001	2	4/24/2026	COMPETING CONTINUATION	$542,999
2026	2021	UNIVERSITY OF LOUISIANA AT LAFAYETTE	104 E UNIVERSITY AVE	LAFAYETTE	LA	70503	LAFAYETTE	USA	Biomedical Research and Research Training	000	1	4/1/2026	NEW	-$51,661
														Subtotal = $491,338

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2021	UNIVERSITY OF LOUISIANA AT LAFAYETTE	104 E UNIVERSITY AVE	LAFAYETTE	LA	70503	LAFAYETTE	USA	Biomedical Research and Research Training	000	1	7/10/2024	NEW	$0
														Subtotal = $0

Issue Date FY: 2021 ( Subtotal = $420,456 )
2021	2021	UNIVERSITY OF LOUISIANA AT LAFAYETTE	104 E UNIVERSITY CIR 3RD FL	LAFAYETTE	LA	70503	LAFAYETTE	USA	Biomedical Research and Research Training	000	1	9/13/2021	NEW	$420,456
														Subtotal = $420,456

Grand Total All Awards = $911,794

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Development of a new TSR algorithm to represent sequences of proteins and 3D structures of nucleotides and molecular complexes for mechanistic understanding of protein sequence and structure relations

Award Number: R15GM144944

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: 09/15/2021

PERIOD OF PERFORMANCE END DATE: 05/31/2029

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