Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

by Łukasz Nierzwicki, Giulia Palermo, Giulia Palermo
Published 2021-04-01

Corrigendum: Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

by Łukasz Nierzwicki, Giulia Palermo, Giulia Palermo
Published 2021-05-01

Systems Biology Modeling of the Complement System Under Immune Susceptible Pathogens

by Nehemiah T. Zewde, Rohaine V. Hsu, Dimitrios Morikis, Giulia Palermo, Giulia Palermo
Published 2021-04-01

Fighting COVID-19 Using Molecular Dynamics Simulations

by Pablo R. Arantes, Aakash Saha, Giulia Palermo
Published 2020-10-01

Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9

by Brandon P. Mitchell, Rohaine V. Hsu, Marco A. Medrano, Nehemiah T. Zewde, Yogesh B. Narkhede, Giulia Palermo, Giulia Palermo
Published 2020-03-01

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems

by Anshuman Kumar, Pablo R. Arantes, Aakash Saha, Giulia Palermo, Bryan M. Wong
Published 2023-01-01

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

by Giulia Palermo, Yinglong Miao, Ross C. Walker, Martin Jinek, J. Andrew McCammon
Published 2016-09-01

Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations

by Jure Borišek, Andrea Saltalamacchia, Anna Gallì, Giulia Palermo, Elisabetta Molteni, Luca Malcovati, Alessandra Magistrato
Published 2019-10-01

Acetylcholine-Binding Protein Affinity Profiling of Neurotoxins in Snake Venoms with Parallel Toxin Identification

by Giulia Palermo, Wietse M. Schouten, Luis Lago Alonso, Chris Ulens, Jeroen Kool, Julien Slagboom
Published 2023-11-01

An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a

by Aakash Saha, Mohd Ahsan, Pablo R. Arantes, Michael Schmitz, Christelle Chanez, Martin Jinek, Giulia Palermo
Published 2024-02-01

Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition

by Yogesh B. Narkhede, Avneesh K. Gautam, Rohaine V. Hsu, Wilson Rodriguez, Nehemiah T. Zewde, Reed E. S. Harrison, Pablo R. Arantes, Zied Gaieb, Ronald D. Gorham, Chris Kieslich, Chris Kieslich, Dimitrios Morikis, Arvind Sahu, Giulia Palermo, Giulia Palermo
Published 2021-03-01

Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets.

by Giulia Palermo, Inga Bauer, Pablo Campomanes, Andrea Cavalli, Andrea Armirotti, Stefania Girotto, Ursula Rothlisberger, Marco De Vivo
Published 2015-06-01

Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

by Giulia Palermo, Alexandre M. J. J. Bonvin, Matteo Dal Peraro, Rommie E. Amaro, Valentina Tozzini, Valentina Tozzini
Published 2020-08-01

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

by Clarisse G. Ricci, Janice S. Chen, Yinglong Miao, Martin Jinek, Jennifer A. Doudna, J. Andrew McCammon, Giulia Palermo
Published 2019-03-01

Allosteric cross-talk in chromatin can mediate drug-drug synergy

by Zenita Adhireksan, Giulia Palermo, Tina Riedel, Zhujun Ma, Reyhan Muhammad, Ursula Rothlisberger, Paul J. Dyson, Curt A. Davey
Published 2017-03-01

Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9

by Lukasz Nierzwicki, Kyle W East, Uriel N Morzan, Pablo R Arantes, Victor S Batista, George P Lisi, Giulia Palermo
Published 2021-12-01

Movement smoothness in chronic post-stroke individuals walking in an outdoor environment-A cross-sectional study using IMU sensors.

by Flora do Vale Garcia, Maira Jaqueline da Cunha, Clarissa Pedrini Schuch, Giulia Palermo Schifino, Gustavo Balbinot, Aline Souza Pagnussat
Published 2021-01-01

Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes

by Jimin Wang, Pablo R. Arantes, Mohd Ahsan, Souvik Sinha, Gregory W. Kyro, Federica Maschietto, Brandon Allen, Erin Skeens, George P. Lisi, Victor S. Batista, Giulia Palermo
Published 2023-01-01

RNA targeting and cleavage by the type III-Dv CRISPR effector complex

by Evan A. Schwartz, Jack P. K. Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, Jennifer S. Brodbelt, Giulia Palermo, Peter C. Fineran, Robert D. Fagerlund, David W. Taylor
Published 2024-04-01

Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

by Elizabeth Brunk, Ivano Tavernelli, Stefano Vanni, Thomas J. Penfold, Giulia Palermo, Marilisa Neri, Marco Micciarelli, Andrey Laktionov, Julian Garrec, Manuel Doemer, Polydefkis Diamantis, Basile F. E. Curchod, F. Franco de Carvalho, Pablo Campomanes, Prashanth Athri, Negar Ashari, Ursula Rothlisberger
Published 2011-09-01