Heterogeneous Solvation in Distinctive Protein–Protein Interfaces Revealed by Molecular Dynamics Simulations von Ricci, Clarisse G, McCammon, J. Andrew

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Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics von Ricci, Clarisse G, Chen, Janice S, Miao, Yinglong, Jinek, Martin, Doudna, Jennifer A, McCammon, J. Andrew, Palermo, Giulia

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Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch von Philpott, Jonathan M, Narasimamurthy, Rajesh, Ricci, Clarisse G, Freeberg, Alfred M, Hunt, Sabrina R, Yee, Lauren E, Pelofsky, Rebecca S, Tripathi, Sarvind, Virshup, David M, Partch, Carrie L

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Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase von G. Ricci, Clarisse, Liu, Yi-Liang, Zhang, Yonghui, Wang, Yang, Zhu, Wei, Oldfield, Eric, McCammon, J. Andrew

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Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9 von Palermo, Giulia, Ricci, Clarisse G, Fernando, Amendra, Basak, Rajshekhar, Jinek, Martin, Rivalta, Ivan, Batista, Victor S, McCammon, J. Andrew

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Docking Studies on DNA-Ligand Interactions: Building and Application of a Protocol To Identify the Binding Mode von Ricci, Clarisse G, Netz, Paulo A

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Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain von Palermo, Giulia, Chen, Janice S., Ricci, Clarisse G., Rivalta, Ivan, Jinek, Martin, Batista, Victor S., Doudna, Jennifer A., McCammon, J. Andrew

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RelA-Containing NFκB Dimers Have Strikingly Different DNA-Binding Cavities in the Absence of DNA von Narang, Dominic, Chen, Wei, Ricci, Clarisse G., Komives, Elizabeth A.

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The invisible dance of CRISPR-Cas9 von Palermo, Giulia, Ricci, Clarisse G., McCammon, J. Andrew

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Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding von Zhang, Zirui, Ricci, Clarisse G, Fan, Chao, Cheng, Li-Tien, Li, Bo, McCammon, J. Andrew

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PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period von Philpott, Jonathan M., Freeberg, Alfred M., Park, Jiyoung, Lee, Kwangjun, Ricci, Clarisse G., Hunt, Sabrina R., Narasimamurthy, Rajesh, Segal, David H., Robles, Rafael, Cai, Yao, Tripathi, Sarvind, McCammon, J. Andrew, Virshup, David M., Chiu, Joanna C., Lee, Choogon, Partch, Carrie L.

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Allosteric Pathways in the PPARγ-RXRα nuclear receptor complex von Ricci, Clarisse G., Silveira, Rodrigo L., Rivalta, Ivan, Batista, Victor S., Skaf, Munir S.

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DNA and IκBα Both Induce Long-Range Conformational Changes in NFκB von Ramsey, Kristen M., Dembinski, Holly E., Chen, Wei, Ricci, Clarisse G., Komives, Elizabeth A.

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The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution von Palermo, Giulia, Ricci, Clarisse G, McCammon, J Andrew

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“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins von Ricci, Clarisse G, Li, Bo, Cheng, Li-Tien, Dzubiella, Joachim, McCammon, J. Andrew

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Molecular Mechanism of Peroxisome Proliferator-Activated Receptor α Activation by WY14643: a New Mode of Ligand Recognition and Receptor Stabilization von Bernardes, Amanda, Souza, Paulo C.T., Muniz, João R.C., Ricci, Clarisse G., Ayers, Stephen D., Parekh, Nili M., Godoy, André S., Trivella, Daniela B.B., Reinach, Peter, Webb, Paul, Skaf, Munir S., Polikarpov, Igor

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Molecular Dynamics of DNA: Comparison of Force Fields and Terminal Nucleotide Definitions von Ricci, Clarisse G, de Andrade, Alex S. C, Mottin, Melina, Netz, Paulo A

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CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands von Mottin, Melina, Souza, Paulo C T, Ricci, Clarisse G, Skaf, Munir S

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Hidden Native State Ensembles of NFκB Dimers Provide Insights into their Different DNA-Binding Affinities von Chen, Wei, Narang, Dominic, Ricci, Clarisse G., Komives, Elizabeth A.

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Remarkable Similarity in Plasmodium falciparum and Plasmodium vivax Geranylgeranyl Diphosphate Synthase (GGPPS) Dynamics and its Implication for Anti-Malarial Drug Design von Venkatramani, Aishwarya, Ricci, Clarisse G., Oldfield, Eric, McCammon, J. Andrew

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