Improving Homology Modeling

While the Protein Data Bank includes nearly 88,000 protein structures that were determined experimentally, there are millions more proteins whose structures are unknown. Comparative or homology modeling offers a powerful approach for leveraging solved structures to reveal important biological details about the others.

Two efforts, both funded through the Protein Structure Initiative, are evaluating the current state of our ability to model protein structures and complexes and seeking ways to further advance the accuracy and usefulness of homology modeling.

GPCR Dock 2013

The NIGMS-funded GPCR Network Exit icon is hosting its third round of the GPCR Docking and Modeling Assessment, GPCR Dock 2013. This assessment of homology modeling and docking methods is focused specifically on G protein-coupled receptors (GPCRs), seven-transmembrane proteins that help transmit essential signals from a wide range of hormones and neurotransmitters in the body and that are a major target of existing drugs. Participants will submit prediction models for four target GPCR-ligand complexes recently determined by GPCR Network investigators and yet to be published. An analysis of the results will be available a few months after the March 3 submission deadline. To participate, register by February 1 Exit icon. For more information, contact the organizers.

Technology Development for Protein Modeling Funding Opportunity

As I stated last month, we have reissued the Technology Development for Protein Modeling (R01) funding opportunity announcement. It encourages grant applications from institutions that propose to develop novel technologies that will significantly improve the accuracy of comparative modeling methods for protein structure prediction. Applicants should focus on one or both of these goals:

  • Near-crystal-structure quality for close homologs of known structures, and/or
  • High-accuracy models for remote homologs of known structures.

Progress Report on the NIGMS Strategic Plan

In 2008, NIGMS issued a strategic plan, Investing in Discovery, that was intended to provide guidance for the Institute over the next 5 years. How well have we done in addressing the plan’s strategic goals? After a critical self-examination, we have produced a progress report that describes some of our accomplishments, strategic decisions and outcomes.

To cite a few highlights, we have:

  • Maintained a funding success rate of approximately 24 percent and funded about 200 new/early-stage investigators each year.
  • Maintained peer review excellence through the implementation and evaluation of innovative review practices.
  • Examined our large-scale science initiatives to determine which to continue, change or phase out, while also ensuring that the resulting knowledge and resources are made widely available to the broader scientific community.
  • Published Investing in the Future, our strategic plan for biomedical and behavioral research training, which articulates a clear, multiyear approach and strategy to ensure that future NIGMS-supported training reflects scientific and workforce needs and contributes to the development of a strong and diverse biomedical research workforce.
  • Established a new Division of Training, Workforce Development, and Diversity, which merges NIGMS research training programs with activities that were previously in the Institute’s Division of Minority Opportunities in Research.
  • Launched this blog to share information about funding opportunities and trends, meetings and scientific resources with our grantees, applicants and others in the scientific community.

I encourage you to read the report for further details and to let us know your thoughts. Although the plan was originally envisioned as a 5-year guide, it is still relevant, and because we hope to have a permanent director later this year, we decided to wait until 2014 to pursue a new strategic planning process.

Advisory Council Meeting

The next meeting of our Advisory Council is later this week. For more information on Council activities, see these previous Feedback Loop posts:

Macromolecular Interactions in Cells, Biomedical Workforce Diversity and Training

You may be interested in these recent funding opportunity announcements:

Revisions for Macromolecular Interactions in Cells (R01)

Purpose: Extend the scientific scope or enhance research capabilities of active NIGMS-funded R01 or R37 projects specializing in the analysis of molecular systems and mechanisms in live organelles, cells, tissues or organisms
Letter of intent due dates: January 19, 2013; August 19, 2013
Application due dates: February 19, 2013; September 19, 2013
NIGMS contacts:
Alexandra Ainsztein, 301-594-0828
Daniel Janes, 301-594-0943
Vernon Anderson, 301-594-3827
Paul Brazhnik, 301-451-6446

Postbaccalaureate Research Education Program (PREP) (R25)

Purpose: Prepare recent baccalaureate science graduates from diverse backgrounds who are underrepresented in biomedical and behavioral sciences to pursue and complete Ph.D. or M.D.-Ph.D. degrees in these fields; and increase the diversity of the host institution’s Ph.D. or M.D.-Ph.D. training programs
Application due date: March 14, 2013
NIGMS contact: Michael Bender, 301-594-0943

Initiative for Maximizing Student Development (IMSD) (R25)

Purpose: Develop new or expand existing institutional developmental programs at research-intensive institutions that prepare undergraduate and graduate students from diverse backgrounds for attaining the Ph.D. degree in biomedical or behavioral sciences and subsequent competitive research careers and leadership positions
Application due date: March 14, 2013
NIGMS contact: Daniel Janes, 301-594-0943

Support of Competitive Research (SCORE) Program, which offers three funding opportunities based on career level that are designed to increase the research competitiveness of faculty at minority-serving institutions and institutions with a historical mission of training students from backgrounds underrepresented in biomedical research

Purpose: Conduct high-quality research and increase research competitiveness by progressively enhancing the pace and productivity of projects
Career level: Advanced formative stage

Purpose: Test a new idea or gather preliminary data to establish a new line of research
Career level: Early academic career

Purpose: Continue engaging in meritorious biomedical or behavioral research projects of limited scope in a given biomedical or behavioral area within the NIH mission
Career level: Intermediate stage

Application due dates: March 4, 2013; May 25, 2013; September 25, 2013
NIGMS contact: Hinda Zlotnik, 301-594-3900

JIT Information: How We Use “Other Support” Data

The study section gave your application a competitive score, and now you’ve been asked to submit Just-in-Time (JIT) information about your other sources of funding, including active and pending support for key personnel on the application. Why do we request this information?

First, for all applications that might be funded, we check the JIT information for scientific overlap with the investigators’ active grants from NIH and other funding sources, since we can’t provide support for a project that’s already being funded.

Second, as directed by the NIGMS Advisory Council, we give additional scrutiny to new and competing renewal applications from investigators whose total research support, including the pending award, exceeds $750,000 or more in annual direct costs. These applications require special analysis and documentation from NIGMS staff to justify why the project is highly meritorious, and they are discussed by the Advisory Council.

Finally, we may use the information about other research support to decide which grants to recommend for funding and to establish the budget level of the award. As you may know, NIGMS does not rely solely on a percentile cutoff or “payline” to make funding decisions. We also consider other factors, including career stage, perceived impact of the proposed work, summary statement comments and the other funding available to the investigator.

I hope this post helps provide some context for how we use JIT information and why it is important that your JIT information is complete, accurate and submitted promptly after the request so as not to delay the funding decision. Additional JIT information is available on the NIH and NIGMS Web sites and from your program director.