image: From left: Charles Christoffer, Genki Terashi and Daisuke Kihara of Purdue University launched the high-tech software startup Molecular Intelligence to determine 3D structures of biomolecules. The software leverages deep learning to analyze cryogenic-electron microscopy data, which consists of 3D image data.
Credit: (Purdue University photo/Pranav Punuru)
WEST LAFAYETTE, Ind. — Purdue University experts in the College of Science and Rosen Center for Advanced Computing have launched Molecular Intelligence, a software company whose solutions help researchers determine the 3D structures of biomolecules imaged with cryogenic-electron microscopy (cryo-EM).
Daisuke Kihara, professor of biological sciences and computer science, leads the company. He also is on the faculty of the Purdue Institute for Cancer Research and Purdue Institute for Drug Discovery. Charles Christoffer, senior computational scientist in the Rosen Center for Advanced Computing, and Genki Terashi, assistant research scientist in the Department of Biological Sciences, are the other founders.
Molecular Intelligence’s end users are research scientists in bioengineering, medical science and pharmaceutical companies who use cryo-EM to determine 3D structures of proteins, nucleic acids and other biomolecules.
“These biomolecular structures provide critical information for understanding how proteins function and for developing drugs, which are designed to interact with proteins and alter their activity,” Kihara said.
Molecular Intelligence was formed in summer 2024. The Purdue Innovates Office of Technology Commercialization issued the company an exclusive license to sell the software in January 2025.
Customers can purchase the software or use the company’s modeling services. For more information, email dkihara@purdue.edu or molintelligence@gmail.com.
The emergence and drawbacks of cryo-EM
Kihara said many academic institutions and pharmaceutical and biotechnology companies worldwide are investing in cryo-EM equipment. More than 1,100 sites have purchased cryo-EMs, and most protein structures are determined by the technology.
But, Kihara said, cryo-EM’s low-resolution image data means building structure models of proteins, nucleic acids and drug molecules is not trivial.
“Current data processing, including structure model building, can take many days, often extending over a couple of weeks, incurring significant costs,” he said. “When a chosen method does not support structure modeling, researchers manually build models using interactive software, which can be time-consuming and error-prone. If a drug target such as a protein is modeled incorrectly, downstream tasks, including drug design, will be significantly hindered.”
The Molecular Intelligence solutions
Kihara, Christoffer and Terashi’s software suite leverages deep learning to analyze cryo-EM data, which consists of 3D image data.
“Deep learning enables the identification of atom positions in low-resolution cryo-EM maps,” Kihara said. “Our software then uses these identified atom positions to construct the 3D structures of proteins and DNA/RNA. No special training is required to use the software; it is automated and runs on a regular workstation with a moderate GPU. We also offer modeling services for users who prefer assistance on our end.”
The research behind Molecular Intelligence’s software has been published in the August 11, 2022; October 2, 2023; and December 8, 2023, issues of Nature Methods and the January 2023 issue of Structural Biology.
The National Institutes of Health provided funding to develop Kihara, Christoffer and Terashi’s computational methods.
Their research and the launch of Molecular Intelligence supports Purdue’s One Health mission, which drives innovation at the intersection of human, animal and plant health.
About Purdue Innovates Office of Technology Commercialization
The Purdue Innovates Office of Technology Commercialization operates one of the most comprehensive technology transfer programs among leading research universities in the U.S. Services provided by this office support the economic development initiatives of Purdue University and benefit the university’s academic activities through commercializing, licensing and protecting Purdue intellectual property. In fiscal year 2024, the office reported 145 deals finalized with 224 technologies signed, 466 invention disclosures received, and 290 U.S. and international patents received. The office is managed by the Purdue Research Foundation, a private, nonprofit foundation created to advance the mission of Purdue University. Contact otcip@prf.org for more information.
About Purdue University
Purdue University is a public research university leading with excellence at scale. Ranked among top 10 public universities in the United States, Purdue discovers, disseminates and deploys knowledge with a quality and at a scale second to none. More than 107,000 students study at Purdue across multiple campuses, locations and modalities, including more than 58,000 at our main campus in West Lafayette and Indianapolis. Committed to affordability and accessibility, Purdue’s main campus has frozen tuition 13 years in a row. See how Purdue never stops in the persistent pursuit of the next giant leap — including its comprehensive urban expansion, the Mitch Daniels School of Business, Purdue Computes and the One Health initiative — at https://www.purdue.edu/president/strategic-initiatives.