Notice of Intent to Publish a Funding Opportunity Announcement for Molecular Dynamics of HIV (R01 Clinical Trial Not Allowed)
Notice Number:

Key Dates

Release Date:
May 16, 2022
Estimated Publication Date of Funding Opportunity Announcement:
August 09, 2022
First Estimated Application Due Date:
December 07, 2022
Earliest Estimated Award Date:
July 01, 2023
Earliest Estimated Start Date:
July 01, 2023
Related Announcements


Issued by

National Institute of Allergy and Infectious Diseases (NIAID)


The National Institutes of Health (NIH) and the National Institute of Allergy and Infectious Diseases (NIAID) intend to publish a Funding Opportunity Announcement (FOA) for applications pertaining to the Molecular Dynamics (MD) of HIV. The purpose of this Funding Opportunity Announcement (FOA) is to support computational dynamic modeling of molecular complexes regulating the HIV life cycle, immune responses, and therapeutic interventions in HIV/AIDS using existing and new HIV and HIV/host cell structural datasets. This Notice is being issued to allow potential applicants more time to consider the requirements of this program and to develop responsive projects.

Research Initiative Details


Molecular Dynamics (MD) simulates the movement of atoms and molecules over time, providing testable models of complex molecular behavior. MD can capture the movement of proteins and other biomolecules in full atomic detail at femtosecond time scales to simulate a variety of biomolecular functions, including ligand or drug binding, protein conformational dynamics, and complex cellular processes like membrane fusion and scission. Multi-scale dynamic modeling extends the scale of simulations to include multi-component complexes or even whole cellular environments. Addition of the dimension of time to the three-dimensional structures already studied by structural biologists can facilitate novel insights into their function. The goal of the modeling is to provide detailed, testable “4D” molecular models depicting dynamic biologic processes. Over the past decade, a large number of high-resolution structures of key HIV and HIV/host cell molecular complexes have been solved. With this initiative, NIAID intends to leverage those accumulating datasets to better understand the dynamic interactions that exist throughout the HIV viral life cycle.

Research Objectives

This initiative will support integrated structural, computational, and functional approaches to study the dynamics of key molecular processes in the HIV life cycle. Applications should address a crucial component of the HIV life cycle, immunological response, or therapeutic intervention that is amenable to structural determination and dynamic modeling. Projects may not be based on purely theoretical modeling of sequence data, but instead should be centered around datasets generated by appropriate atomic or molecular scale approaches such as NMR, electron microscopy or optical techniques. Research projects should include iterative biologic testing and refinement of the computational models to generate an accurate and rigorous model system. Approaches affording insight at all cellular scales, from atomistic to whole-cell resolutions, are encouraged. Development of new technological innovation in modeling approaches and computational processes is highly desired, as are projects that leverage machine learning / artificial intelligence to facilitate analyses. Research teams should include computational modelers along with structural biologists, virologists, immunologists or other appropriate expertise to validate model systems. Applications that propose vertebrate animal research and/or clinical research are allowed.

Examples of research foci of interest include but are not limited to:

  • HIV Env-mediated receptor binding and membrane fusion
  • HIV capsid interactions with cytoplasmic and nuclear transport machinery
  • HIV transcription, latency, and epigenetic regulation
  • HIV genomic RNA recognition and recruitment to sites of viral assembly
  • HIV assembly, budding and release
  • HIV recognition by and escape from innate immune factors
  • Binding of HIV antigens to B-cell surface Immunoglobulin receptors
  • Affinity maturation of anti-HIV neutralizing antibodies
  • Mechanisms of action of novel anti-HIV therapeutics and their interactions with host or viral targets

Applications meeting the following conditions will be considered non-responsive and will not be reviewed:

  • Applications that are not primarily focused on dynamic modeling of HIV/host cell structural data relevant to NIAID research priorities of HIV prevention, treatment, and cure
  • Applications that only involve theoretical modeling of protein/nucleic acid sequences or other biological data without a focus on experimental structural datasets
  • Applications that do not include functional analyses and testing of hypotheses derived from the modeling simulations
  • Applications that propose a clinical trial

Applicant organizations may submit more than one application, provided that each application is scientifically distinct.

Foreign (non-US) applications and domestic applications with foreign components will be permitted.

Funding Information


Estimated Total Funding


Expected Number of Awards

NIAID intends to fund 3-5 awards.

Estimated Award Ceiling

Application budgets are limited to $500,000 in direct costs and should reflect the actual needs of the proposed project

Primary Assistance Listing Number(s)


Anticipated Eligible Organizations
Public/State Controlled Institution of Higher Education
Private Institution of Higher Education
Nonprofit with 501(c)(3) IRS Status (Other than Institution of Higher Education)
Small Business
For-Profit Organization (Other than Small Business)
State Government
Indian/Native American Tribal Government (Federally Recognized)
County governments
Independent school districts
Public housing authorities/Indian housing authorities
Indian/Native American Tribally Designated Organization (Native American tribal organizations (other than Federally recognized tribal governments)
U.S. Territory or Possession
Indian/Native American Tribal Government (Other than Federally Recognized)
Regional Organization
Eligible Agencies of the Federal Government

Applications are not being solicited at this time. 


Please direct all inquiries to:

David McDonald, Ph.D.

National Institute of Allergy and Infectious Diseases (NIAID)