# Nanoscale programing of cellular and physiological phenotypes Equipment

> **NIH NIH R35** · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · 2020 · $96,000

## Abstract

ABSTRACT
The long and expensive trial-and-error drug discovery process resulted in a profoundly slow pace of discovery
of novel biologically active compounds. Computational molecular docking-based virtual screening provides an
efficient and significantly less expensive approach to identify the drug-like lead compounds, which, upon further
chemical modifications, yield drugs that can be used in therapy. However, even with state-of-the-art high-
performance computational clusters, the drug virtual screening process still takes months. Furthermore, the
accuracy of the virtual screening highly depends on the ability of virtual screening tools to mimic flexibility of the
complex when drug is binding to its target, thereby making accuracy and speed of virtual screening to strongly
depend on each other. We have previously developed a rapid and flexible protein-ligand docking program
MedusaDock, which lays a solid foundation for virtual screening. Using MedusaDock, we have already
discovered and in a process of commercialization of compounds for cystic fibrosis and pain. Here, we propose
to extend MedusaDock to support Graphics Processing Units (GPUs) acceleration in order to leverage the
powerful computing performance of GPUs and thereby expedite the virtual screening process. We have initiated
research on porting MedusaDock to GPUs, which offer massive serialization of processes. In our preliminary
studies, we have already improved the speed by a factor 3.5x. We expect larger improvement upon completio n
of the algorithms that utilize GPUs. Here, we request for supplemental funding of a GPU cluster to perform such
simulations. This cluster will be shared with our colleague Dr. Ed O’Brien in the Department of Chemistry. Adding
the ability to utilize GPU clusters will create new opportunities for virtual drug screening campaigns and will help
us identify new small molecule regulators of protein function.

## Key facts

- **NIH application ID:** 10134689
- **Project number:** 3R35GM134864-01S1
- **Recipient organization:** PENNSYLVANIA STATE UNIV HERSHEY MED CTR
- **Principal Investigator:** NIKOLAY DOKHOLYAN
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $96,000
- **Award type:** 3
- **Project period:** 2020-01-01 → 2024-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10134689

## Citation

> US National Institutes of Health, RePORTER application 10134689, Nanoscale programing of cellular and physiological phenotypes Equipment (3R35GM134864-01S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10134689. Licensed CC0.

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