*co-first author  corresponding author


Screen Shot 2021-11-29 at 10.39.22 AM49. Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9. Ł. Nierzwicki, K. W. East, U. N. Morzan, P. R. Arantes, V. S. Batista, G. P. Lisi and d G. Palermo. BiorXiv preprint 2021

48. Structural and Dynamic Insights into the HNH Nuclease of Divergent Cas9 Species. H. B. Belato, A. M. D’Ordine, Ł. Nierzwicki, P. R. Arantes, G. Jogl, G. Palermo and G. P. Lisi.† J. Struct. Biol. 2021, accepted.

Screen Shot 2021-07-17 at 12.54.42 PM47. J. Manigrasso, M. De Vivo and G. Palermo. Controlled Trafficking of Multiple Cations Prompt Nucleic Acid Hydrolysis. ACS Catalysis 2021, 11, 14, 8786–8797. JOURNAL COVER ART.

46. N. T. Zewde, R. V. Hsu. D. Morikis and G. Palermo. Systems Biology Modeling of the Complement System Under Immune Susceptible Pathogens. Front. Phys. 2021, 9, 603704.

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Ł. Nierzwicki and G. Palermo. Molecular Dynamics to predict Cryo-EM: capturing transitions and short-lived conformational states of biomolecules. Front. Mol. Biosci. 2021, 8:641208. 

TOC_GaMD-vFinal44. J. Wang,* P. R. Arantes,* A. Bhattarai, R. V. Hsu, S. Pawnikar, Y. M. Huang, G. Palermo and Y. Miao.† Gaussian accelerated molecular dynamics (GaMD): principles and applications. WIREs Comp. Mol. Sci. 2021, e1521. 

logo_wid151943. N. Farag, R. Mattossovich, R. Merlo, Ł. Nierzwicki, G. Palermo, A. Porchetta, G. Peruginoand F. Ricci.† Folding-upon-repair DNA nanoswitches for monitoring DNA repair enzymes activity. Angew. Chem. Int. Ed. 2021, 133, 2-9.

42. G. Palermo, A. Spinello, A. Saha, and A. Magistrato. Frontiers of Metal-coordinating Drug Design. Expert Opin. Drug. Disc. 2021, 1-15.

41. Y. B. Narkhede,* A. K. Gautam,* R. V. Hsu,* W. Rodriguez, N. T. Zewde, R. E. S. Harrison, P. R. Arantes, Z. Gaieb, R. D. Gorham Jr, C. Kieslich, D. Morikis, A. Sahu and G. Palermo. Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins toward Human and Bovine Complement Inhibition. Front. Mol. Biosci. 2021, 8:618068. 


Screen Shot 2020-10-06 at 5.13.57 PM40. L. Casalino, Ł. Nierzwicki, M. Jinek and G. Palermo. Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab-Initio Molecular Dynamics. ACS Catalysis, 2020, 22, 13596-13605. JOURNAL COVER ART.

piccolino39. K. W. East, J. C. Newton, U. N. Morzan, Y. B. Narkhede, A. Acharya, E. Skeens, G. Jogl, V. S. Batista, G. Palermo and G. P. Lisi.Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. J. Am. Chem. Soc. 2020, 142, 1348-1358. Featured in the JACS 2021 Early Investigators Virtual Issue!

38. Ł. Nierzwicki, P. R. Arantes, A. Saha and G. Palermo. Establishing the Allosteric Mechanism in CRISPR-Cas9. WIREs Comp. Mol. Biosci. 2020, e1503.

A. Saha,* P. R. Arantes,* R. V. Hsu, Y. B. Narkhede, M. Jinek and G. Palermo.Molecular Dynamics Reveal a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. J. Chem. Inf. Model. 2020, 60, 6427–6437. ACS Editors’ Choice. JOURNAL COVER ART.

36. P. R. Arantes, A. Saha and G. Palermo. Fighting COVID-19 Using Molecular Dynamics Simulations. First Reaction, ACS Cent. Sci. 2020, 6, 1654–1656.

35. J. Cui, F. Zhang, Ł. Nierzwicki, G. Palermo, R. Linhardt and G. P. Lisi.† Mapping the Structural and Dynamic Determinants of pH-sensitive Heparin Binding to Granulocyte Macrophage-colony Stimulating Factor. Biochemistry 2020, 59, 3541–3553.

34. B. P. Mitchell, R. V. Hsu, M. A. Medrano, N. T. Zewede, Y. B. Narkhede, G. Palermo.  Spontaneous embedding of DNA mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Front. Mol. Biosci. 2020, 7, 39.

33. R. E. H. Harrison, N. T. Zewde, Y. B. Narkhede, R. V. Hsu, D. Morikis, V. Vullev and G. Palermo. Factor-H Inspired Design of Peptide Biomarkers of the Complement C3d Protein. ACS Med. Chem. Lett. 2020, 11, 1054-1059. 

Untitled32. K. W. East, E. Skeens, J. Y. Cui, H. B. Belato, B. P. Mitchell, R. V. Hsu, V. S. Batista, G. Palermo, G. P. Lisi. NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes. Biophys. Rev. 2020, 1-20 .



31. S. Vanni, L. Riccardi, G. Palermo  and M. De Vivo.† Structure and dynamics of the acyl chains in the membrane trafficking and enzymatic processing of lipids. Acc. Chem. Res. 2019, 52, 3087-3096. JOURNAL COVER ART. 

micio30. G. Palermo. Structure and Dynamics of the CRISPR-Cas9 Catalytic Complex. J. Chem. Inf. Model. 2019, 59, 2394-2406. JOURNAL COVER ART.

29. G. Palermo. Dissecting Structure and Function of DNA:RNA Hybrids. Chem 2019, 5, 1364-1366


28. C. G. Ricci, J. S. Chen, Y. Miao, M. Jinek, J. A. Doudna, J. A. McCammon and G. Palermo. Deciphering Off-target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent. Sci. 2019, 5, 651-662.

27. J. Borisek, A. Saltalamacchia, A. Galli, G. Palermo, E. Molteni, L. Malcovati, A. Magistrato.Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations. Biomolecules 2019, 9, 633

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26. G. Palermo, C. G. Ricci and J. A. McCammon. The invisible dance of CRISPR-Cas9. Molecular simulations unveil the molecular side of the gene-editing revolution. Physics Today, 2019, 72, 4, 30.

X1047847725. G. Palermo, L. Casalino, A. Magistrato and J. A. McCammon. Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations. J. Struct. Biol. 2019, 206, 267-279. JOURNAL COVER ART. Awarded 1st Place Prize at the Image Contest of the 2017 Biophysical Society Annual Meeting!


24. S. J. Wodak. et Al. Allostery in its many disguises: from theory to applications. Structure 2019, 4, 566-578.


23. L. Casalino, G. Palermo, A. Spinello, U. Rothlisberger and A. Magistrato. All-Atom Simulations Disentangle the Functional Dynamics Underlying Gene Maturation in the Intron Lariat Spliceosome. Proc. Natl. Acad. Sci. USA 2018, 115, 6584-6589.

Screen Shot 2020-07-29 at 9.04.39 PM22. G. Palermo, J. S. Chen, C. G. Ricci, I. Rivalta, M. Jinek, V. S. Batista, J. A. Doudna and J. A. McCammon. Key role of the REC lobe during CRISPR-Cas9 activation by “sensing”, “regulating” and “locking” the catalytic HNH domain. Quarterly Rev. Biophys. 2018, 51, e9.

Before UCR

TOC4-121. G. Palermo, C. G. Ricci, A. Fernando, R. Basak, M. Jinek, I. Rivalta, V. S. Batista and J. A. McCammon PAM-induced allostery activates CRISPR-Cas9. J. Am. Chem. Soc. 2017, 139, 16028–16031. JOURNAL COVER ART. Featured in the JACS 2018 Early Investigators Virtual Issue!

20. G. Palermo, Y. Miao, R. C. Walker, M. Jinek and J. A. McCammon. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc. Natl. Acad. Sci. USA. 2017, 114, 7260–7265.


19. Z. Adhireksan,* G. Palermo,* T. Riedel,* Z. Ma, R. Muhammad, P. J. Dyson, U. Rothlisberger and C. A. Davey. Allosteric cross-talk in chromatin can mediate drug-drug synergy. Nat. Commun. 2017, 8, 14860.

pero18. N. Ashari Astani, S. Meloni, A. H. Salavati, G. Palermo, M. Graetzel, U. Rothlisberger. Computational Characterization of the Dependence of Halide Perovskite Effective Masses on Chemical Composition and Structure. J. Phys. Chem. C. 2017, 121, 23886–23895.  

17. L. Casalino, G. Palermo, N. Abdurakhmonova, U. Rothlisberger and A. Magistrato. Development of Site-specific Mg-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations. J. Chem. Theory Comput. 201713, 340–352. 

Untitled16. G. Palermo, Y. Miao, R. C. Walker, M. Jinek and J. A. McCammon. Striking plasticity of CRISPR-Cas9 and key role of non-target DNA, as revealed from molecular simulations. ACS Cent. Sci. 20162, 756–763. First computer simulations of CRISPR-Cas9. Awarded Best Use of HPC in Life sciences. 


15. Z. Ma,* G. Palermo,* Z. Adhireksan,* B. S. Murray, T. von Erlach, P. J. Dyson, U. Rothlisberger and C. A. Davey. An Organometallic Compound Displays a Unique One-Stranded Intercalation Mode that is DNA Topology-Dependent. Angew. Chem. Int. Ed. 2016, 128, 7441–7444.

Journal of the American Chemical Society

14. L. Casalino, G. Palermo, U. Rothlisberger and A. Magistrato. Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns. J. Am. Chem. Soc2016, 138, 10374–10377. JOURNAL COVER ART.

object01813. S. Meloni, G. Palermo, N. Ashari Astani, M. Graetzel and U. Rothlisberger. Valence and conduction bands engineering in halide perovskites for solar cell applications. J. Mater. Chem. A. 2016, 4, 1599716002.

12. G. Palermo, A. Magistrato, T. Riedel, T. von Erlach, C. A. Davey, P. J. Dyson and U. Rothlisberger. Fighting cancer with organometallic compounds: from naked DNA to protein and chromatin targeting strategies. ChemMedChem, 2016, 11, 11991210. Special Issue on Polypharmacology and Multitarget Drugs.

11. G. Palermo, A. D. Favia, M. Convertino and M. De Vivo. The molecular basis for dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) inhibition. ChemMedChem, 2016, 11, 12521258.

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10. G. Palermo, A. Cavalli, M. L. Klein, M. Alfonso Prieto, M. Dal Peraro and M. De Vivo. Catalytic metal ions and enzymatic processing of DNA and RNA. Acc. Chem. Res. 2015, 48, 220–228. 


9. G. Palermo, I. Bauer, P. Campomanes, A. Cavalli, A. Armirotti, S. Girotto, U. Rothlisberger and M. De Vivo. Keys to lipid selection in FAAH catalysis: structural flexibility, gating residues, and multiple binding pockets. PLoS Comput. Biol. 2015, 11, e1004231. JOURNAL COVER ART.

Untitled8. G. Palermo, E. Minniti, M. L. Greco, L. Riccardi, E. Simoni, M. Convertino, C. Marchetti, M. Rosini, C. Sissi, A. Minarini and M. De Vivo. An optimized polyamine moiety boosts potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14152. Chem. Commun. 2015, 51, 14310

7. G. PalermoP. Campomanes, A. Cavalli, U. Rothlisberger and M. De Vivo. Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion. J. Phys. Chem. B. 2015, 119, 789801. Prof. W. Jorgensen Festschrift. JOURNAL COVER ART.

6. G. Palermo, A. Cavalli, U. Rothlisberger and M. De Vivo. Computational insights into function and inhibition of the Fatty Acid Amide Hydrolase (FAAH). Eur. J. Med. Chem. 2015, 91, 15–26.

5. G. Palermo, P. Campomanes, M. Neri, D. Piomelli, A. Cavalli, U. Rothlisberger and M. De Vivo. Wagging the tail: essential role of substrate flexibility in FAAH catalysis. J. Chem. Theory. Comput. 2013, 15, 1202–1213.

4. G. Palermo, M. Stenta, A. Cavalli, M. Dal Peraro and M. De Vivo. Molecular simulations highlight the role of metals in catalysis and inhibition of type II topoisomerase. J. Chem. Theory. Comput. 2013, 9, 857–862. JOURNAL COVER ART.

3. G. Palermo, D. Branduardi, M. Masetti, A. Lodola, M. Mor, D. Piomelli, A. Cavalli and M. De Vivo. Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas. J. Med. Chem. 2011, 54, 66126623.  

2. E. Brunk, N. Ashari, P. Athri, P. Campomanes, F. F. de Carvalho, B. F. Curchod, P. Diamantis, M. Doemer, J. Garrec, A. Laktionov, M. Micciarelli, M. Neri, G. Palermo, T. J. Penfold, S. Vanni, I. Tavernelli and U. Rothlisberger. Pushing frontiers of first-principles based computer simulations of chemical and biological systems. Chimia (Aarau), 2011, 65, 667671. 


 1. G. Palermo, R. Riccio and G. Bifulco. Effect of Electronegative Substituents and Angular Dependence on the Heteronuclear Spin-Spin Coupling Constant 3JC-H: An Empirical Prediction Equation Derived by Density Functional Theory Calculations. J. Org. Chem. 2010, 7, 1982–1991.

Other Publications

Journal of Chemical Information and Modeling5. G. Palermo, Y. Sugita, W. Wriggers and R. E. Amaro. Faces of Contemporary CryoEM Information and Modeling. J. Chem. inf. Model. 2020, 60, 2407-2409.

4. A. Palermo, L. Casalino & G. Palermo.† Vincent Van Gogh’ Autocatalysis. The Art of Theoretical Biology, Springer Nature 2020, 114-115. 


3. G. Palermo, K. A. Armacost and M. Nagan. Women Make COMP: Mentoring the Next-Generation of Women in Computational Chemistry. Viewpoint in J. Chem. Inf. Model. 2019, 59, 4061-4062. 

2. G. Palermo, Y. Sugita, W. Wriggers and R. E. Amaro. Frontiers in CryoEM Modeling. Editorial in J. Chem. Inf. Model. 2019, 59, 3091-3093. 

1. G. Palermo and M. De Vivo. Computational Methods for Drug Discovery. Book chapter in Encyclopedia of Nanotechnology, 2nd Ed. Springer, Heidelberg, 2015, 1-15.

Communications to Conferences (main)

  • 2020, October. Keynote speaker NICE International Conference 2020 (FR)
  • 2020, August. Four talks at the ACS Virtual Meeting and Expo (USA)
  • 2020, August. Invited talk at the “International COVID-19 Knowledge Exchange virtual meeting”.
  • 2020, July. Invited talk at the “Italian Young Medicinal Chemistry Virtual Meeting”.
  • 2020, June. Talk at the Virtual Meeting “Challenges in RNA modeling and design” Telluride (CO).
  • 2020, February. Invited talk at the “Molecular Machines and Assemblies” subgroup, 64th Biophysical Society annual meeting, San Diego (US) 
  • 2019, September. Invited talk at the “RNA Informatics” conference, Hinxton (UK)
  • 2019, September. Invited talk at the “Structure Based Drug Design” conference, Genova (IT)
  • 2019, August. Three talks at the 258th ACS National Meeting, San Diego (USA)
  • 2019, April. Two talks at the 257th ACS national meeting in Orlando (FL).
  • 2019, March. Talk at the 63th Biophysical Society Meeting, Baltimore (USA)
  • 2018, December. Talk at the 2nd International conference on CRISPR technologies. San Diego (USA)
  • 2018, August. Talk at the 256th ACS National Meeting, Boston (USA)
  • 2018, July. Invited speaker at the workshop “Challenges in RNA Structural Modeling and Design” at the Telluride Science Research Center, Telluride (USA).
  • 2018, May. Invited speaker at the CECAM workshop “Physiological role of ions in the brain: toward a comprehensive understanding via molecular simulations”, Scuola Normale Superiore, Pisa (IT)
  • 2018, February. Nominee at the “Future of Biophysics Burroughs Wellcome Fund Symposium” at the 62nd Biophysical Society Meeting, San Francisco (USA)
  • 2017, November. Invited speaker at the CECAM workshop “Computational approaches to investigating allostery”, Lausanne (CH)
  • 2017, September. Talk at the conference “Computational Advances in Drug Discovery”, Lausanne (CH)
  • 2017, April. Four talks at the 253th ACS National Meeting, San Francisco (USA).
  • 2017, February. Poster at the 61th Biophysical Society Meeting, New Orleans (USA)
  • 2017, January. Poster at the 11th symposium on RNA biology, SALK institute, La Jolla (CA, USA)
  • 2016, May. Talk at the “Structural and Functional Annotation of Bioinorganic Systems: Perspectives and Challenges from Theory and Experiments” workshop, Scuola Normale Superiore, Pisa (IT)
  • 2016, March. Two talks at the 251th ACS National Meeting, San Diego (USA)
  • 2016, February. Talk and poster at the 60th Biophysical Society Meeting, Los Angeles (USA). Co-chair with Prof. A. Dickson.
  • 2015, June. Talk at the “Modeling activity vs. selectivity in metalloproteins” workshop, CECAM, Paris (FR).
  • 2015, February. Talk and the 59th Biophysical Society Meeting, Baltimore (USA).
  • 2014, November. Talk at the “Advanced modeling to investigate biomolecules” workshop, CECAM, Genova (IT)
  • 2014, August. 248th ACS National Meeting, San Francisco (USA).
  • 2014, April. Talk at the 245th ACS National Meeting, New Orleans (USA).
  • 2013, October. Talk at the “Innovative Approaches to Computational Drug Discovery” workshop,  CECAM, Lausanne (CH).
  • 2013, February. Talk at the II Computationally Driven Drug Discovery Meeting,  CECAM, Genova (IT).

Invited Talks (main)

  • 2020, April. Invited talk at the University of Texas at Austin. 
  • 2020, March. Invited talk at Georgia State University. 
  • 2019, November. Invited talk at the University of Southern California. 
  • 2018, September. Invited talk at Imperial College London.
  • 2019, March. Invited talk at University of Idaho. 
  • 2019, March. Invited talk at the University of Florida. 
  • 2019, February. Invited talk at Washington University in St. Louis. 
  • 2019, February. Invited talk at the University of Rochester. 
  • 2019, February. Invited talk at Max Plank Institute Berlin. 
  • 2019, January. Invited talk at The Scripps Research Institute, La Jolla. 
  • 2019, January. Invited talk at California Institute of Technology.  
  • 2016, September. Invited talk at the Heidelberg Institute of Theoretical Studies (Heidelberg, DE). 
  • 2016, September. Invited talk at the University of Zürich (CH). 
  • 2015, October. Selected talk for the ETH post-doc day 2015. Swiss Federal Institute of Technology – Zurich.
  • 2015, March. Invited talk  at the Institute for Advanced Simulations, Forschungszentrum Jülich (Jülich – DE). 
  • 2015, February. Invited talk  at the San Diego Super Computer Center, University of California San Diego (CA – USA). 
  • 2015, February. Invited talk  at University of Chicago, department of Biochemistry, Chicago (Illinois – USA).
  • 2014, December. Invited talk  at the International School of Advanced Studies (SISSA), Trieste (IT).