Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level. - Pablo D. Dans; Leonardo Darré; Matías R. Machado; Ari Zeida; Astrid F. Brandner; Sergio Pantano (BSB, 2013)

SIRAH tools: mapping, backmapping and visualization of coarse-grained models. - Matías R. Machado; Sergio Pantano (Bioinform., 2016)

Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly. - Juan Francisco Viso; Patricia Belelli; Matías R. Machado; Humberto González; Sergio Pantano; María Julia Amundarain; Fernando Zamarreño; Maria Marta Branda; Diego M. A. Guérin; Marcelo D. Costabel (PLoS Comput. Biol., 2018)

Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. - Martín Soñora; Leandro Martínez; Sergio Pantano; Matías R. Machado (J. Chem. Inf. Model., 2021)

AmberTools. - David A. Case; Hasan Metin Aktulga; Kellon Belfon; David S. Cerutti; G. Andrés Cisneros; Vinícius Wilian D. Cruzeiro; Negin Forouzesh; Timothy J. Giese; Andreas W. Götz; Holger Gohlke; Saeed Izadi; Koushik Kasavajhala; et al. (J. Chem. Inf. Model., 2023)