# Simulation of  Multi-Protein systems

> **NIH NIH R01** · STATE UNIVERSITY NEW YORK STONY BROOK · 2021 · $310,763

## Abstract

Simulation of large multi-component molecular assemblies with atomistic details is an important
step toward understanding cellular processes. The goal of this proposal is to develop an
efficient method for the simulation of multi-protein systems consisting of many copies of a few
types of proteins, each in a number of discrete conformations. The basis for our approach is the
observation that the interaction energy between two proteins (or discrete protein conformations
within an ensemble) – can be efficiently calculated over the entire rotational-translational space
using the fast Manifold Fourier transform (FMFT) correlation approach. Given any conformation
of a complex multi-particle system, its energy can be easily obtained by summing the pairwise
interaction energies extracted from the lookup tables. The key innovation to efficiently
implement this method is our ability to compress and store the interaction energy lookup tables
in memory using wavelet sets. We will apply the method in two application. The first is
simulation of multi-protein assemblies and their association pathways, possibly in conjunction
with low resolution Mass Spectrometry (MS) and EM data, providing mechanistic insight into
cellular function. The second is simulation of protein aggregation and crowding, which is
important for the fundamental understanding of cell biology and therapeutic development.

## Key facts

- **NIH application ID:** 10100198
- **Project number:** 1R01GM140098-01
- **Recipient organization:** STATE UNIVERSITY NEW YORK STONY BROOK
- **Principal Investigator:** Dmytro Kozakov
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $310,763
- **Award type:** 1
- **Project period:** 2021-09-20 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10100198

## Citation

> US National Institutes of Health, RePORTER application 10100198, Simulation of  Multi-Protein systems (1R01GM140098-01). Retrieved via AI Analytics 2026-06-14 from https://api.ai-analytics.org/grant/nih/10100198. Licensed CC0.

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