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How does protein structure guide biomolecular interactions and protein function?

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What we do

We strive to characterize molecular interactions within and between proteins, including their substrates, antibodies, and small molecule compounds using structural and computational biology. We leverage our thorough understanding of these molecular interactions to develop clinically relevant solutions, including designing and optimizing inhibitors.

How we do it

We synergistically utilize experimental and computational techniques to gain fundamental insights into molecular recognition events involving protein-protein and protein-ligand interactions. Much of our work focuses on developing design strategies for drug candidates against resistant viruses, but we also apply this framework to other diseases such as cancer and Type I Diabetes.

Why we do it

Beyond our passion for fundamental molecular and structural biology, we are motivated by our goal of contributing to the development of new treatment options for various human diseases.



Research Highlights

a ball and stick illustration of protease inhibitorsStructural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease

Ozen, A., Lin, K.H., Kurt Yilmaz, N., Schiffer, C.A. (2014) Proc. Natl. Acad. Sci.

While evolving high levels of resistance to protease inhibitors, HIV-1 accumulates mutations not only in the protease but also its substrates. In this work we revealed the molecular-level interplay between these two types of resistance mutations, and how co-evolution of the substrate restores the structure and dynamics of the complex to allow evolution of resistant viral variants.


an illustration of various inhibitors binding to a proteinAvoiding drug resistance by substrate envelope guided design: toward potent and robust HCV NS3/4A protease inhibitors

Matthew, A.N., Zephyr, J., Rao, D.N., Henes, M., Kamran, W., Kosovrasti, K., Hedger, A.K., Lockbaum, G.J., Ali, A., Kurt Yilmaz, N., Shiffer, C.A. (2020) mBio

Leveraging our knowledge of the intermolecular interaction between HCV NS3/4A protease and its natural substrates, we designed improved inhibitors that display better potency against clinically relevant resistant variants of the virus. These lessons are transferable to the design of potent and robust inhibitors against other dug targets.


graphical abstract from avnir 2017 showing a protein binding multiple other proteinsStructural determination of the broadly reactive anti-IGHV1-69 anti-idiotypic antibody G6 and its idiotope

Avnir, Y., ..., Kurt Yilmaz, N., Schiffer, C.A., Marasco, W.A. (2017) Cell Reports

Anti-idiotypic antibodies are those that bind to other antibodies with critical implications for response to infection and vaccination. In this work, structural modeling and analysis helped explain experimentally observed specificity and reactivity of the anti-idiotypic antibody G6, which binds to anti-influenza stem-directed broadly neutralizing antibodies.

Contact Us


Campus Map (pdf)

508-856-1867 (office)


Mailing Address:
UMass Chan Medical School
Attn: Nese Kurt Yilmaz, PhD
Associate Professor
Department of Biochemistry & Molecular Biotechnology
364 Plantation Street, LRB 970-J
Worcester MA, 01605-2324

Join Us

Undergraduates interested in pursuing a PhD at UMass Chan Medical School should apply directly to the Morningside Graduate School of Biomedical Sciences Program.