# Computational Biology Core

> **NIH NIH P01** · UNIVERSITY OF CINCINNATI · 2024 · $182,060

## Abstract

SUMMARY (Core B)
One of the key strengths of this Program Project is the powerful reciprocal relationship of in silico modeling and
simulation with targeted structural and functional experimentation. Thus, experimental results can be
channeled back into in situ studies to iteratively improve models. The overarching goal of the Computational
Biology Core (Core B) is to take advantage of information from the literature, experimental results from our
Program, and ab initio modeling to create, and continually improve, molecularly detailed structural models and
functional hypotheses for each step, and each major player, in cholesterol efflux. The core is structured to
provide the following services: 1) create model structures and perform several varieties of molecular dynamics
(MD) simulations of molecular models—SMD, CGMD, STMD—relevant to each Project; 2) refine structures of
ABCA1, APOA1, and various HDL particles generated during the previous PPG cycle; 3) provide a platform for
comparing molecular models to experimental data (chemical crosslinking, HDL particle sizes derived from ion
mobility analyses, HDL composition, etc.). One primary tool will be construction of protein contact maps; 4) use
LOCATE to analyze and refine the molecular basis for interactions of amphipathic helical domains of APOA1,
APOA2, and other apolipoproteins with each other as well as their interactions with ABCA1; 5) use Rosetta for
ab initio modeling and docking (e.g. APOA1’s interactions with ABCA1; APOA2’s interactions with APOA1,
etc.). Core B will be led by Jere Segrest, MD, PhD, working closely with Hyun Song, PhD, at Vanderbilt
University Medical Center campus, near where Project 3 is located. Both investigators have extensive, well-
documented expertise in all areas of the Core’s proposed services. In the previous PPG cycle, the Core
executed thousands of hours of computer simulations that generated dozens of detailed molecular models for
experimental testing by all three Projects. Many of these models will contribute critically to the ongoing studies
proposed in this renewal cycle.

## Key facts

- **NIH application ID:** 10903856
- **Project number:** 5P01HL128203-07
- **Recipient organization:** UNIVERSITY OF CINCINNATI
- **Principal Investigator:** Jere P Segrest
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $182,060
- **Award type:** 5
- **Project period:** 2016-09-15 → 2028-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10903856

## Citation

> US National Institutes of Health, RePORTER application 10903856, Computational Biology Core (5P01HL128203-07). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10903856. Licensed CC0.

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