# Molecular Modeling

> **NIH NIH P41** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2021 · $416,242

## Abstract

III. TR&D1 - Abstract
The last decade has seen the creation of a remarkably inventive array of approaches for 4D modeling
of biomolecular systems, using coarse-grained models and enhanced-sampling methods, as well as
spatiotemporally realistic approaches at cellular scale. However, “mesoscale” systems such as large
multi-protein complexes and subcellular structures, and “omics-scale” systems like chromatin have
received significantly less attention. There is a surging need to develop computational technology for
structure-based mesoscopic- and spatially resolved omics-scale modeling. Several methodologies
already developed by TR&D1 investigators show great promise for meeting this need. These include
the methods and tools based on elastic network models (ENMs) and implemented in the ProDy
Application Programming Interface (API) developed for modeling supramolecular systems dynamics,
and the Armatus software developed for identifying topological associated domains in chromosomes.
Our goal is to further develop these and other innovative technologies that we developed during the
past term, such as weighted-ensemble (WE)-based methods and software (WESTPA) for enhancing
simulation efficiency applicable to both molecular and cellular scales, toward addressing these newly
emerging challenges. Our research and development activities will be driven by four Driving Biomedical
Projects that will focus on the complex interactions controlling neurotransmission and neurosignaling
events (DBP1-3), and on constructing a spatial dynamic map of transcription and chromatin structure
(DBP6). We will work together with all three other TR&Ds to meet the multiscale challenges of the
investigated complex systems and processes. Our aims are formulated as (1) advancing and
implementing the methodology for treating the structure, dynamics, and interactions of multimeric
proteins and multiprotein assemblies, (2) extending our computing capabilities to modeling
chromosomal structure, dynamics and function, and (3) further development of TR&D1 high-
performance computing (HPC) platform under the Bridges environment provided by the PSC, to ensure
efficient integration of all software within TR&D1, as well as interoperability with those developed at the
other three TR&Ds, and at other Resources pursuing complementary goals.

## Key facts

- **NIH application ID:** 10228747
- **Project number:** 5P41GM103712-10
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** Ivet Bahar
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $416,242
- **Award type:** 5
- **Project period:** 2012-09-24 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10228747

## Citation

> US National Institutes of Health, RePORTER application 10228747, Molecular Modeling (5P41GM103712-10). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10228747. Licensed CC0.

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