# Modeling and Interacting with the Visible Molecular Cell

> **NIH NIH R01** · SCRIPPS RESEARCH INSTITUTE, THE · 2020 · $473,405

## Abstract

Project Summary/Abstract
It is now possible to approach the structural modeling and visualization of entire cells
with detail at the atomic level. In this project, we will expand the capabilities of
cellPACK, a method for creating integrative 3D models of cellular environments,
bridging from the level of atoms to the level of cells. These models will provide
unprecedented possibilities for the understanding of cellular function and disease states,
enabling new opportunities for intervention. They will also challenge several aspects of
the technologies needed to generate, visualize and interactively explore very large 3D
and 4D structural datasets. Our goal is to develop the modeling and visualization tools
that enable others to develop, run and analyze dynamic simulations of these complex
models. Several critical barriers must be overcome to make this effort a successful tool
for research and scientific education, including the management of large informational
databases, methods for the automated modeling of the structure and interaction of
soluble, fibrous, and membrane-bound molecular assemblies in crowded cellular
environments, and comprehensible visualization of, and interaction with these large and
heterogenous models. We will approach these challenges with four specific aims:
1) Procedural methods for mesoscale modeling of complex assemblies, such as the
 bacterial nucleoid, peptidoglycan, lipopolysaccharide, and polysomes;
2) Computer-assisted tools for the management of complex multiscale data for
 specifying 3D mesoscale models of cells;
3) Development of fast and effective methods to allow display of and interaction with
 these complex mesoscale models;
4) Application of these methods to research in bacterial biology and creation of a Google
 Earth inspired viewer for use in education and outreach.

## Key facts

- **NIH application ID:** 9975197
- **Project number:** 5R01GM120604-05
- **Recipient organization:** SCRIPPS RESEARCH INSTITUTE, THE
- **Principal Investigator:** DAVID S GOODSELL
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $473,405
- **Award type:** 5
- **Project period:** 2016-09-15 → 2021-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9975197

## Citation

> US National Institutes of Health, RePORTER application 9975197, Modeling and Interacting with the Visible Molecular Cell (5R01GM120604-05). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9975197. Licensed CC0.

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