Selected Publications

Cruz MA, Frederick TE, Mallimadugula UL, Singh S, Vithani N, Zimmerman MI, Porter JR, Moeder KE, Amarasinghe GK, Bowman GR.: A cryptic pocket in Ebola VP35 allosterically controls RNA binding. Nat Commun 13: 2269, Apr 2022.

Jansen J, Reimer KC, Nagai JS, Varghese FS, Overheul GJ, de Beer M, Roverts R, Daviran D, Fermin LAS, Willemsen B, Beukenboom M, Djudjaj S, von Stillfried S, van Eijk LE, Mastik M, Bulthuis M, Dunnen WD, van Goor H, Hillebrands JL, Triana SH, Alexandrov T, Timm MC, van den Berge BT, van den Broek M, Nlandu Q, Heijnert J, Bindels EMJ, Hoogenboezem RM, Mooren F, Kuppe C, Miesen P, Grünberg K, Ijzermans T, Steenbergen EJ, Czogalla J, Schreuder MF, Sommerdijk N, Akiva A, Boor P, Puelles VG, Floege J, Huber TB; COVID Moonshot consortium, van Rij RP, Costa IG, Schneider RK, Smeets B, Kramann R.: SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell Stem Cell 29: 217-231, Feb 2022.

Topf M, Rosta E, Bowman GR, Bonomi M.: Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function. Front Mol Biosci 8: 799406, Nov 2021.

Knoverek CR, Mallimadugula UL, Singh S, Rennella E, Frederick TE, Yuwen T, Raavicharla S, Kay LE, Bowman GR.: Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proc Natl Acad Sci U S A 118: e2106473118, Nov 2021.

Malik M, Ward MD, Fang Y, Porter JR, Zimmerman MI, Koelblen T, Roh M, Frolova AI, Burris TP, Bowman GR, Imoukhuede PI, England SK.: Naturally Occurring Genetic Variants in the Oxytocin Receptor Alter Receptor Signaling Profiles. ACS Pharmacol Transl Sci 4: 1543-1555, Sep 2021.

Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR.: SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophys J 120: 2880-2889, Jul 2021.

Ward MD, Zimmerman MI, Meller A, Chung M, Swamidass SJ, Bowman GR.: Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets. Nat Commun 12: 3023, May 2021.

Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS.: The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 12: 1936, Mar 2021.

Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR.: SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nat Chem 13: 651–659, 2021.

Kshirsagar M, Tasnina N, Ward MD, Law JN, Murali TM, Lavista Ferres JM, Bowman GR, Klein-Seetharaman J.: Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 -human interactome. Pac Symp Biocomput 26: 154-165, 2021.