Selected Publications

Dixon, T., MacPherson, D., Mostofian, B., Rajat Pal et al. Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry. Nat Commun 13, 5884 (2022). Download PDF

Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat K. Pal, and Emilio Gallicchio. Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. J. Chem. Inf. Model. 62, 309 (2022).  Download PDF

Rajat Kumar Pal, Emilio Gallicchio. Perturbation Potentials to Overcome Order/Disorder Transitions in Alchemical Binding Free Energy Calculations. arXiv:1907.06636v2 [q-bio.BM] J. Chem. Phys. 151, 124116 (2019).  Download PDF

Rajat Kumar Pal, Steve Ramsey, Satishkumar Gadhiya, Pierpaolo Cordone, Lauren Wickstrom, Wayne W. Harding, Tom Kurtzman, Emilio Gallicchio. Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes. arXiv:1904.11058v1 [physics.bio-ph] PLoS ONE 14(9): e0222902 (2019).  Download PDF

Rajat Kumar Pal, Kamran Haider, Divya Kaur, William Flynn, Junchao Xia, Ronald M Levy, Tetiana Taran, Lauren Wickstrom, Tom Kurtzman, Emilio Gallicchio. A Combined Treatment of Hydration and Dynamical Effects for the Modeling of Host-Guest Binding Thermodynamics: The SAMPL5 Blinded Challenge. J. Comp. Aided. Mol. Des. 31, 29 (2016) 31:29-44.  Download PDF

Murelli, R. P.; D'Erasmo, M. P.; Hirsch, D. R.; Meck, C.; Masaoka, T.; Wilson, J. A.; Zhang, B.; Pal, R. K.; Gallicchio, E.; Beutler, J. A.; Le Grice, S. F. J. Synthetic α-Hydroxytropolones as Inhibitors of HIV Reverse Transcriptase Ribonuclease H Activity. Med. Chem. Commun., 2016, Sep 1; 7(9): 1783–1788.  Download PDF