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Saha, A.; Arantes, P. R.; Ahsan, M.; Jinek, M.; Palermo, G. An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nat. Comm. 2024, 15, 1473.
Saha, A.; Arantes, P. R.; Palermo, G. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Curr. Opin. Struct. Biol. 2022, 75, 102400.
Saha, A.; Arantes, P. R.; Hsu, R. V.; Narkhede, Y. B.; Jinek, M.; Palermo, G. Molecular dynamics reveal a DNA-induced dynamic switch triggering activation of CRISPR-Cas12a. J. Chem. Inf. Model 2020, 60, 6427-6437.
Saha, A.; Pindi, C.; Palermo, G. The synchronized catalytic dance of CRISPR-Cas9. Nature Catalysis 2023, 6, 870-872.
Strohkendl, I.; Saha, A.; Moy, C.; Nguyen, A. H.; Ahsan, M.; Russell, R.; Palermo, G.; Taylor, D.W. Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Molecular Cell 2024, 84, 1-15.
Arantes, P.*; Chen, X.*; Sinha, S.*; Saha, A.*; Patel, A.; Sample, M.; Nierzwicki, Ł; Lapinaite, A.; Palermo, G. Biophysical origin of improved base editing efficiency in CRISPR-Cas9–conjugated ABE enzymes. Nucleic Acids Res. 2024, gkae1066.
Pacesa, M.; Lin, C. H.; Cléry A.; Saha, A.; Arantes, P. R.; Bargsten K.; Irby M. J.; Allain F. H. T.; Palermo, G; Cameron P.; Donohouse P. D.; Jinek M. Structural basis for Cas9 off-target activity. Cell 2022, 185, 4067-4081.
Newman, A.; Saha, A.; Starrs, L.; Arantes, P. R.; Palermo, G.; Burgio, G. CRISPR-Cas12a REC2–NUC interactions drive target-strand cleavage and constrain trans cleavage. bioRxiv 2025 (under review).
Zhao, H.; Velez, C.; Naravane, A. C.; Saha, A.; Feldman, J.; Skolnick, J.; Murray, D.; Honig, B. Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks. bioRxiv 2025 (under review).
Rossetti, M.; Merlo, R.; Bagheri, N.; Moscone, D.; Valenti, A.; Saha, A; Arantes, P. R.; Ippodrino, R.; Ricci, F.; van der Oost, J.; Palermo, G.; Perugino, G.; Porchetta, A. Rational design of hairpin DNA reporters for enhanced CRISPR/Cas12a trans-cleavage activity. Nucleic Acids Res. 2022, 50, 8377-8391.
Fan, X.; Ye, Y.; Saha, A.; Peng, L.; Pindi, C.; Wang, Q.; Yang, L.; Liu, J.; Tang, X.; Palermo, G.; Liao, J.; Xu, T.; Lu, Y.; Du, G. Fine-tuning pH sensor H98 by remote essential residues in the hydrogen-bond network of mTASK-3. Int. J. Biol. Macromolecules 2024, 273, 132892.
Kumar, A; Arantes, P.R.; Saha, A; Palermo, G; Wong, B. M. GPU-Enhanced DFTB metadynamics for efficiently predicting free energies of biochemical systems. Molecules 2023, 28, 1277.
Nierzwicki, Ł; Arantes, P. R.; Saha, A.; Palermo G. Establishing the allosteric mechanism in CRISPR-Cas9. WIREs Comp. Mol. Biosci. 2021, 11, e1503.
Palermo, G.; Spinello A.; Saha, A.; Magistrato, A. Frontiers of metal-coordinating drug design. Expert Opin. Drug Discovery 2021, 16, 497-511.
Arantes P. R.; Saha A.; Palermo G. Fighting COVID-19 using molecular dynamics simulations. ACS Cent. Sci. 2020, 6, 1654-1656.
Ahsan, M.; Saha, A.; Nierzwicki, Ł; Palermo, G. Molecular dance of CRISPR-Cas9 with divalent metal ions. In preparation.
Saha, A.; Pal, A.; Goswami, R. Preventive effect of curcumin against cisplatin-related hepatotoxicity in Swiss Albino mice (Mus musculus L.). J. Chem. Pharma. Sci. 2018, 11, 255-260.
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