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Items: 15

1.

The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution.

Palermo G, Ricci CG, McCammon JA.

Phys Today. 2019 Apr;72(4):30-36. doi: 10.1063/PT.3.4182.

2.

Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.

Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G.

ACS Cent Sci. 2019 Apr 24;5(4):651-662. doi: 10.1021/acscentsci.9b00020. Epub 2019 Mar 7.

3.

Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA.

Q Rev Biophys. 2018;51. pii: e91. doi: 10.1017/S0033583518000070. Epub 2018 Aug 3.

4.

Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations.

Ricci CG, McCammon JA.

J Phys Chem B. 2018 Dec 13;122(49):11695-11701. doi: 10.1021/acs.jpcb.8b07773. Epub 2018 Oct 9.

5.

RelA-Containing NFκB Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA.

Narang D, Chen W, Ricci CG, Komives EA.

J Mol Biol. 2018 May 11;430(10):1510-1520. doi: 10.1016/j.jmb.2018.03.020. Epub 2018 Apr 3.

6.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly.

Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA.

Front Mol Biosci. 2018 Feb 12;5:13. doi: 10.3389/fmolb.2018.00013. eCollection 2018. Review.

7.

Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9.

Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA.

J Am Chem Soc. 2017 Nov 15;139(45):16028-16031. doi: 10.1021/jacs.7b05313. Epub 2017 Aug 7.

8.

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA.

J Phys Chem B. 2017 Jul 13;121(27):6538-6548. doi: 10.1021/acs.jpcb.7b04113. Epub 2017 Jun 27.

9.

DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB.

Ramsey KM, Dembinski HE, Chen W, Ricci CG, Komives EA.

J Mol Biol. 2017 Apr 7;429(7):999-1008. doi: 10.1016/j.jmb.2017.02.017. Epub 2017 Feb 27.

10.

CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands.

Mottin M, Souza PC, Ricci CG, Skaf MS.

Int J Mol Sci. 2016 Dec 22;18(1). pii: E15. doi: 10.3390/ijms18010015.

11.

Allosteric Pathways in the PPARγ-RXRα nuclear receptor complex.

Ricci CG, Silveira RL, Rivalta I, Batista VS, Skaf MS.

Sci Rep. 2016 Jan 29;6:19940. doi: 10.1038/srep19940.

12.

Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization.

Bernardes A, Souza PC, Muniz JR, Ricci CG, Ayers SD, Parekh NM, Godoy AS, Trivella DB, Reinach P, Webb P, Skaf MS, Polikarpov I.

J Mol Biol. 2013 Aug 23;425(16):2878-93. doi: 10.1016/j.jmb.2013.05.010. Epub 2013 May 21.

13.

Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions.

Ricci CG, de Andrade AS, Mottin M, Netz PA.

J Phys Chem B. 2010 Aug 5;114(30):9882-93. doi: 10.1021/jp1035663.

PMID:
20614923
14.

Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode.

Ricci CG, Netz PA.

J Chem Inf Model. 2009 Aug;49(8):1925-35. doi: 10.1021/ci9001537.

PMID:
19655805
15.

A thrombin inhibitor from the gut of Boophilus microplus ticks.

Ricci CG, Pinto AF, Berger M, Termignoni C.

Exp Appl Acarol. 2007;42(4):291-300. Epub 2007 Aug 21.

PMID:
17710557

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