Clarisse Gravina Ricci
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Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode
CG Ricci, PA Netz
Journal of chemical information and modeling 49 (8), 1925-1935, 2009
Protospacer adjacent motif-induced allostery activates CRISPR-Cas9
G Palermo, CG Ricci, A Fernando, R Basak, M Jinek, I Rivalta, VS Batista, ...
Journal of the American Chemical Society 139 (45), 16028-16031, 2017
Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization
A Bernardes, PCT Souza, JRC Muniz, CG Ricci, SD Ayers, NM Parekh, ...
Journal of molecular biology 425 (16), 2878-2893, 2013
Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain
G Palermo, JS Chen, CG Ricci, I Rivalta, M Jinek, VS Batista, JA Doudna, ...
Quarterly Reviews of Biophysics 51, 1-11, 2018
Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions
CG Ricci, ASC de Andrade, M Mottin, PA Netz
The Journal of Physical Chemistry B 114 (30), 9882-9893, 2010
Deciphering off-target effects in CRISPR-Cas9 through accelerated molecular dynamics
CG Ricci, JS Chen, Y Miao, M Jinek, JA Doudna, JA McCammon, ...
ACS central science 5 (4), 651-662, 2019
Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch
JM Philpott, R Narasimamurthy, CG Ricci, AM Freeberg, SR Hunt, LE Yee, ...
Elife 9, e52343, 2020
Allosteric Pathways in the PPARγ-RXRα nuclear receptor complex
CG Ricci, RL Silveira, I Rivalta, VS Batista, MS Skaf
Scientific Reports 6 (1), 19940, 2016
A thrombin inhibitor from the gut of Boophilus microplus ticks
CG Ricci, AFM Pinto, M Berger, C Termignoni
Experimental and Applied Acarology 42, 291-300, 2007
DNA and IκBα both induce long-range conformational changes in NFκB
KM Ramsey, HE Dembinski, W Chen, CG Ricci, EA Komives
Journal of molecular biology 429 (7), 999-1008, 2017
PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period
JM Philpott, AM Freeberg, J Park, K Lee, CG Ricci, SR Hunt, ...
Molecular Cell 83 (10), 1677-1692. e8, 2023
The invisible dance of CRISPR-Cas9
G Palermo, CG Ricci, JA McCammon
Physics today 72 (4), 30-36, 2019
RelA-Containing nfκb dimers have strikingly different DNA-Binding cavities in the absence of DNA
D Narang, W Chen, CG Ricci, EA Komives
Journal of molecular biology 430 (10), 1510-1520, 2018
“Martinizing” the variational implicit solvent method (VISM): solvation free energy for coarse-grained proteins
CG Ricci, B Li, LT Cheng, J Dzubiella, JA McCammon
The Journal of Physical Chemistry B 121 (27), 6538-6548, 2017
Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase
CG Ricci, YL Liu, Y Zhang, Y Wang, W Zhu, E Oldfield, JA McCammon
Biochemistry 55 (36), 5180–5190, 2016
Simulation of the interactions between Tröger bases and DNA
CG Ricci, PA Netz
Journal of the Brazilian Chemical Society 23, 1334-1346, 2012
Coupling Monte Carlo, variational implicit solvation, and binary level-set for simulations of biomolecular binding
Z Zhang, CG Ricci, C Fan, LT Cheng, B Li, JA McCammon
Journal of chemical theory and computation 17 (4), 2465-2478, 2021
Tailoring the variational implicit solvent method for new challenges: Biomolecular recognition and assembly
CG Ricci, B Li, LT Cheng, J Dzubiella, JA McCammon
Frontiers in molecular biosciences 5, 13, 2018
Heterogeneous Solvation in Distinctive Protein–Protein Interfaces Revealed by Molecular Dynamics Simulations
CG Ricci, JA McCammon
The Journal of Physical Chemistry B 122 (49), 11695-11701, 2018
Remarkable similarity in Plasmodium falciparum and Plasmodium vivax geranylgeranyl diphosphate synthase dynamics and its implication for antimalarial drug …
A Venkatramani, C Gravina Ricci, E Oldfield, JA McCammon
Chemical biology & drug design 91 (6), 1068-1077, 2018
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Articles 1–20