Borna Novak

MSTP in PhD Training

Program: Computational and Systems Biology

Current advisor: Alex Holehouse, PhD

Undergraduate university: University of Sciences-Philadelphia, 2019

Enrollment year: 2019

Research summary
Exploring the Sequence-Ensembe Relationship of Intrinsically Disordered Proteins

A large fraction of proteins from the human proteome are classified as Intrinsically Disordered Proteins (IDPs). These proteins exhibit significant variability in their conformational states, lacking a stable, predefined three-dimensional structure. Instead, they undergo rapid transitions among a diverse set of configurations. Understanding the relationship between IDP’s sequences and their ensemble of conformations is crucial for deciphering their biological function. To gain insights into this relationship, I am employing a combination of computer simulations and bioinformatics. This interdisciplinary approach aims to uncover how the sequence of an IDP influences its conformational ensemble, ultimately shedding light on its functional properties.

Graduate publications
Meller A, Lotthammer JM, Smith LG, Novak B, Lee LA, Kuhn CC, Greenberg L, Leinwand LA, Greenberg MJ, Bowman GR. 2023 Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains. Elife, 12():e83602. PMCID: PMC9995120

Chung MKJ, Miller RJ, Novak B, Wang Z, Ponder JW. 2023 Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. J Chem Inf Model, 63(9):2769-2782. PMCID:

Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. 2021 SARS-CoV2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophys J, ():S0006-3495(21)00254-X. PMCID: PMC8007187