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IMP: Software for Hybrid Determination of Macromolecular Assembly Structures

Award Number: R01GM083960
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: 04/01/2008
PERIOD OF PERFORMANCE END DATE: 08/31/2026

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IMP: Software for Hybrid Determination of Macromolecular Assembly Structures - Project Summary The broad goal is to develop and apply computational methods for building structural models of proteins and their assemblies. One successful approach, integrative structure modeling, casts the building of such models as a computational optimization problem where knowledge about the assembly is encoded into the scoring function used to evaluate candidate models. We propose to extend and enhance the Integrative Modeling Platform (IMP) program that provides programmatic support for developing and distributing integrative structure modeling pro- tocols. IMP already allows representing molecules at multiple resolutions, using spatial restraints from many types of data, and searching for solutions by a variety of sampling algorithms. So far, it has been applied mostly to data from electron microscopy (EM), mass spectrometry, small angle X-ray scattering, Förster resonance energy transfer, crosslinking, hydrogen deuterium exchange (HDX), and various proteomics methods. IMP is easily extensible to add support for new data sources and algorithms, and is distributed under an open source license. Here, we propose to extend IMP to address a greater range of biological problems and make it more generally useful to the scientific community. Specifically, in Aim 1, we will develop integrative threading for computing an atomic model based on a density map determined at medium resolution (4-8 Å) by EM or X- ray crystallography. This goal will be achieved by simultaneously sampling both threading and conformation based on the density map as well as other data, such as chemical cross-links and HDX protection factors. This method is significant because it will produce atomic resolution models from medium-resolution maps determined by either EM or X-ray crystallography. In Aim 2, we will develop a Bayesian integrative method for modeling ensembles of similar systems. Data from different samples, ensembles, and/or variants are often pooled together to model a single representative structure. This synthesis is problematic when the variation between the actual structures across the samples, ensembles, and variants is larger than the uncertainty of the data. We will address the challenge by developing a general and flexible scheme for representing and scoring related structural en- sembles. This method is significant because it will improve the accuracy of the model and the estimate of its uncertainty. In Aim 3, we will maximize the impact of IMP on the community, by delivering a well-tested and maintained software package that is documented with mailing lists, examples, and demonstrations at local and external workshops, by hosting select users at UCSF, and by pursuing closer integration with other software packages and community resources, including databases such as the Protein Data Bank (PDB), structure view- ers such as Chimera and VMD, and other modeling programs such as NAMD and ReaDDy. The proposed aims are informed by and will shape the nascent worldwide PDB effort on representing, validating, archiving, and disseminating integrative structure models.


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: 2025 ( Subtotal = $0 )
2025	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	16	8/27/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2024 ( Subtotal = $342,380 )
2024	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	16	9/18/2024	NON-COMPETING CONTINUATION	$342,380
														Subtotal = $342,380

Issue Date FY: 2023 ( Subtotal = $342,380 )
2023	2023	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	15	8/2/2023	NON-COMPETING CONTINUATION	$342,380
														Subtotal = $342,380

Issue Date FY: 2022 ( Subtotal = $541,660 )
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	003	14	9/21/2022	SUPPLEMENT FOR EXPANSION	$199,280
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	002	14	8/30/2022	NON-COMPETING CONTINUATION	$342,380
2022	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	13	7/12/2022	COMPETING CONTINUATION	$63,856
2022	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	12	7/12/2022	NON-COMPETING CONTINUATION	-$63,856
														Subtotal = $541,660

Issue Date FY: 2021 ( Subtotal = $342,380 )
2021	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	13	8/30/2021	COMPETING CONTINUATION	$342,380
2021	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	12	8/20/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $342,380

Issue Date FY: 2020 ( Subtotal = $326,510 )
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	12	1/9/2020	NON-COMPETING CONTINUATION	$326,510
														Subtotal = $326,510

Issue Date FY: 2019 ( Subtotal = $326,510 )
2019	2019	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	11	12/14/2018	NON-COMPETING CONTINUATION	$326,510
														Subtotal = $326,510

Issue Date FY: 2018 ( Subtotal = $326,510 )
2018	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 420	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	10	5/7/2018	NON-COMPETING CONTINUATION	$32,651
2018	2018	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 420	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	10	11/27/2017	NON-COMPETING CONTINUATION	$293,859
														Subtotal = $326,510

Issue Date FY: 2017 ( Subtotal = $326,510 )
2017	2017	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	9	12/9/2016	COMPETING CONTINUATION	$326,510
2017	2017	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 420	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	003	9	5/12/2017	COMPETING CONTINUATION	$65,096
2017	2015	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 420	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	002	8	5/12/2017	NON-COMPETING CONTINUATION	-$65,096
2017	2015	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	8	12/6/2016	NON-COMPETING CONTINUATION	$0
														Subtotal = $326,510

Issue Date FY: 2015 ( Subtotal = $309,000 )
2015	2015	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	8	3/12/2015	NON-COMPETING CONTINUATION	$309,000
														Subtotal = $309,000

Issue Date FY: 2014 ( Subtotal = $309,000 )
2014	2014	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	7	4/21/2014	NON-COMPETING CONTINUATION	$309,000
														Subtotal = $309,000

Issue Date FY: 2013 ( Subtotal = $298,185 )
2013	2013	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	6	6/12/2013	NON-COMPETING CONTINUATION	$20,085
2013	2013	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	6	3/29/2013	NON-COMPETING CONTINUATION	$278,100
														Subtotal = $298,185

Issue Date FY: 2012 ( Subtotal = $309,000 )
2012	2012	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	5	3/29/2012	COMPETING CONTINUATION	$309,000
2012	2011	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	4	3/28/2012	NON-COMPETING CONTINUATION	$0
														Subtotal = $309,000

Issue Date FY: 2011 ( Subtotal = $272,566 )
2011	2011	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	4	3/28/2011	NON-COMPETING CONTINUATION	$247,787
2011	2011	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	001	4	6/6/2011	NON-COMPETING CONTINUATION	$24,779
														Subtotal = $272,566

Issue Date FY: 2010 ( Subtotal = $275,319 )
2010	2010	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	3	3/31/2010	NON-COMPETING CONTINUATION	$275,319
														Subtotal = $275,319

Issue Date FY: 2009 ( Subtotal = $278,100 )
2009	2009	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	2	4/1/2009	NON-COMPETING CONTINUATION	$278,100
														Subtotal = $278,100

Issue Date FY: 2008 ( Subtotal = $277,875 )
2008	2008	UNIVERSITY OF CALIFORNIA-SAN FRANCISCO	BOX 0812	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Biomedical Research and Research Training	000	1	3/7/2008	NEW	$277,875
														Subtotal = $277,875

Grand Total All Awards = $5,203,885

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IMP: Software for Hybrid Determination of Macromolecular Assembly Structures

Award Number: R01GM083960

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: 04/01/2008

PERIOD OF PERFORMANCE END DATE: 08/31/2026

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