SIRAH tools: mapping, backmapping and visualization of coarse-grained models von Machado, Matías R, Pantano, Sergio

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Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations von Machado, Matías R, Pantano, Sergio

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Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane–Protein Dynamics von Barrera, Exequiel E, Machado, Matías R, Pantano, Sergio

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The SIRAH 2.0 Force Field: Altius, Fortius, Citius von Machado, Matías R, Barrera, Exequiel E, Klein, Florencia, Sóñora, Martín, Silva, Steffano, Pantano, Sergio

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FRET biosensor uncovers cAMP nano-domains at β-adrenergic targets that dictate precise tuning of cardiac contractility von Surdo, Nicoletta C., Berrera, Marco, Koschinski, Andreas, Brescia, Marcella, Machado, Matias R., Carr, Carolyn, Wright, Peter, Gorelik, Julia, Morotti, Stefano, Grandi, Eleonora, Bers, Donald M., Pantano, Sergio, Zaccolo, Manuela

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Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus von Soñora, Martín, Martínez, Leandro, Pantano, Sergio, Machado, Matías R

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Fighting viruses with computers, right now von Machado, Matías R, Pantano, Sergio

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Thiol-based chemical probes exhibit antiviral activity against SARS-CoV-2 via allosteric disulfide disruption in the spike glycoprotein von Shi, Yunlong, Zeida, Ari, Edwards, Caitlin E, Mallory, Michael L, Sastre, Santiago, Machado, Matías R, Pickles, Raymond J, Fu, Ling, Liu, Keke, Yang, Jing, Baric, Ralph S, Boucher, Richard C, Radi, Rafael, Carroll, Kate S

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Nitro-fatty acids as activators of hSIRT6 deacetylase activity von Carreño, Mara, Bresque, Mariana, Machado, Matías R., Santos, Leonardo, Durán, Rosario, Vitturi, Darío A., Escande, Carlos, Denicola, Ana

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Hitting the Detection Limit in cAMP Signaling von Klein, Florencia, Machado, Matías R, Pantano, Sergio

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A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics von Dans, Pablo D, Zeida, Ari, Machado, Matías R, Pantano, Sergio

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MD Simulations of Viruslike Particles with Supra CG Solvation Affordable to Desktop Computers von Machado, Matı́as R, González, Humberto C, Pantano, Sergio

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From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field von Machado, Matías R, Zeida, Ari, Darré, Leonardo, Pantano, Sergio

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Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? von Darré, Leonardo, Machado, Matías R, Dans, Pablo D, Herrera, Fernando E, Pantano, Sergio

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Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay von Rego, Natalia, Salazar, Cecilia, Paz, Mercedes, Costábile, Alicia, Fajardo, Alvaro, Ferrés, Ignacio, Perbolianachis, Paula, Fernández-Calero, Tamara, Noya, Veronica, Machado, Matias R, Brandes, Mariana, Arce, Rodrigo, Arleo, Mailen, Possi, Tania, Reyes, Natalia, Bentancor, María Noel, Lizasoain, Andrés, Bortagaray, Viviana, Moller, Ana, Chappos, Odhille, Nin, Nicolas, Hurtado, Javier, Duquía, Melissa, González, Maria Belén, Griffero, Luciana, Méndez, Mauricio, Techera, Maria Pía, Zanetti, Juan, Pereira, Emiliano, Rivera, Bernardina, Maidana, Matías, Alonso, Martina, Smircich, Pablo, Arantes, Ighor, Mir, Daiana, Alonso, Cecilia, Medina, Julio, Albornoz, Henry, Colina, Rodney, Bello, Gonzalo, Moreno, Pilar, Moratorio, Gonzalo, Iraola, Gregorio, Spangenberg, Lucía

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Coarse-grained models of water von Darré, Leonardo, Machado, Matías R., Pantano, Sergio

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AmberTools von Case, David A., Aktulga, Hasan Metin, Belfon, Kellon, Cerutti, David S., Cisneros, G. Andrés, Cruzeiro, Vinícius Wilian D., Forouzesh, Negin, Giese, Timothy J., Götz, Andreas W., Gohlke, Holger, Izadi, Saeed, Kasavajhala, Koushik, Kaymak, Mehmet C., King, Edward, Kurtzman, Tom, Lee, Tai-Sung, Li, Pengfei, Liu, Jian, Luchko, Tyler, Luo, Ray, Manathunga, Madushanka, Machado, Matias R., Nguyen, Hai Minh, O’Hearn, Kurt A., Onufriev, Alexey V., Pan, Feng, Pantano, Sergio, Qi, Ruxi, Rahnamoun, Ali, Risheh, Ali, Schott-Verdugo, Stephan, Shajan, Akhil, Swails, Jason, Wang, Junmei, Wei, Haixin, Wu, Xiongwu, Wu, Yongxian, Zhang, Shi, Zhao, Shiji, Zhu, Qiang, Cheatham, Thomas E., Roe, Daniel R., Roitberg, Adrian, Simmerling, Carlos, York, Darrin M., Nagan, Maria C., Merz, Kenneth M.

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SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation von Garay, Pablo G., Machado, Matias R., Verli, Hugo, Pantano, Sergio

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CUTie2: The Attack of the Cyclic Nucleotide Sensor Clones von Klein, Florencia, Sardi, Florencia, Machado, Matías R, Ortega, Claudia, Comini, Marcelo A, Pantano, Sergio

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New Insights into the Role of the Trypanosoma cruzi Aldo-Keto Reductase TcAKR von Díaz-Viraqué, Florencia, Chiribao, María Laura, Paes-Vieira, Lisvane, Machado, Matias R., Faral-Tello, Paula, Tomasina, Ramiro, Trochine, Andrea, Robello, Carlos

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