Bioengineering Ph.D. Student Receives National Recognition for Breakthrough Molecular Computational Tool

Nandhini Rajagopal’s accomplishments are massive even though her research focuses on small molecules. As part of biomedical and chemical engineering Professor Shikha Nangia’s research group, the Ph.D. student has focused her work on minute interactions between protein molecules in the biological cells that make up all living things. These interactions between proteins are essential since proteins are the building blocks of all living things.  Rajagopal’s work is entirely computational and as part of her research she developed a new algorithm that could determine how two different protein molecules would interact.

“These small proteins are found in every tissue of our body,” says Rajagopal. “Using computers we literally visualize how these molecules move around each other and aggregate.”

Rajagopal’s computational tool can screen all possible orientations for how two proteins would interact with each other.

“How proteins interact has a direct impact on their functions,” says Rajagopal. “I wanted to create an algorithm that would also plot a graph showing an intuitive, easy-to-interpret three-dimensional energy landscape of the two interacting protein molecules.”

“The algorithm produces not only highly accurate results, it is also highly efficient. Nandhini’s algorithm can sample millions of protein-protein interactions in a matter of minutes, which otherwise used to take weeks to simulate,” says Nangia.

Rajagopal was selected to present her computational method at the 2020 Gordon Research Conference (GRC), a premier scientific conference where a select group of researchers meet to discuss cutting-edge research in biological, chemical and physical sciences. Rajagopal’s presentation was well received by the experts in the field and led to multiple national and international collaborations.

The algorithm was published in the Journal of Chemical Theory and Computation and featured on the cover. For her outstanding work, Rajagopal won several notable awards:

  • 2021 Merck Research Award from the American Chemical Society (ACS) Women Chemistry Committee
  • 2020 ACS Chemical Computing Group Excellence Award for Graduate Students
  • 2021 All University Doctoral Prize from the College of Engineering and Computer Science.
  • 2021 Outstanding Graduate Student in Bioengineering
  • 2021 Research Presentation Award, College of Engineering and Computer Science Research Day
  • 2020 Syracuse University Graduate Student Award for Distinguished Biomaterials Research

Rajagopal is finishing up an externship at Genentech’s pharmaceutical development division and will begin a postdoctoral research position at pharmaceutical company Boehringer Ingelheim this summer.

She hopes to continue her current research and see how it could expand to cancer studies.

“With the new algorithm, we can decipher how interactions between proteins can be altered and could aid in finding new drugs for diseases whose treatment options were elusive. I am extremely proud of the Nandhini’s innovation,” says Nangia.