Publications

Publications

2024

• J. Cantero, A. Ballesteros-Casallas, L. H. Santos, M. Paulino, S. Pantano. Pouring SIRAH on NAMD. The Journal of Physical Chemistry B 2024, 1520-6106.


• P. G. Garay, M. R. Machado, H. Verli, S. Pantano. SIRAH Late Harvest: Coarse-Grained Models for Protein Glycosylation. Journal of Chemical Theory and Computation 2024, 20, 2, 963–976.

2023

• E. N. Frigini, R. D. Porasso, T. Beke-Somfai, J. J. López Cascales, R. D. Enriz, S. Pantano. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. Journal of Chemical Information and Modeling 2023, 63, 6877-6889.


• L. Borges-Araújo, I. Patmanidis, A. P. Singh, L. H. S. Santos, A. K. Sieradzan, S. Vanni, C. Czaplewski, S. Pantano, W. Shinoda, L. Monticelli, A. Liwo, S. J. Marrink, P. C. T. Souza. Pragmatic coarse-graining of proteins: models and applications. Journal of Chemical Theory and Computation 2023, 19, 7112-7135.


• F. Klein, M. Soñora, L. H. Santos, E. N. Frigini, A. Ballesteros-Casallas, M. R. Machado, S. Pantano. The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels. Journal of Structural Biology 2023, 10, 79-85.


• E. E. Barrera, S. Pantano. Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBER. BOOK CHAPTER: A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules 2023.


• A. Rayevsky, E. Bulgakov, M. Sharifi, D. Samofalova, D. Ozheredov, Pavel Karpov, S. Pantano, Y. Blume. In silico induced effect of N-ε-lysine acetylation on microtubule stability and subsequent interaction of microtubule-associated proteins. Cell Biology International 2023, 47, 1547–1557.

2022

• M, Soñora, E. E. Barrera, S. Pantano. The stressed life of a lipid in the Zika virus membrane. Biochimica et Biophysica Acta (BBA)-Biomembranes 2022, 1864, 1, 183804.

2021

• P. G. Garay, E. E. Barrera, F. Klein, M. R. Machado, M. Soñora, S. Pantano. The SIRAH-CoV-2 Initiative: a coarse-grained simulations' dataset of the sars-cov-2 proteome. Frontiers in Medical Technology 2021, 3, 1, 644039.


• M. Soñora, L. Martinez, S. Pantano, M. R. Machado. Wrapping up viruses at multiscale resolution: optimizing PACKMOL and SIRAH execution for simulating the zika virus. Journal of Chemical Information and Modeling 2021, 61, 1, 408-422.


• F. Klein, E. E. Barrera, S. Pantano. Assessing SIRAH’s capability to simulate intrinsically disordered proteins and peptides. Journal of chemical theory and computation 2021, 17, 2, 599-604.


• M. R. Machado, S. Pantano. Fighting viruses with computers, right now. Current Opinion in Virology 2021, 48, 91-99.


• E. E. Barrera, F. Zonta, S. Pantano. Dissecting the role of glutamine in seeding peptide aggregation. Computational and Structural Biotechnology Journal 2021, 19, 1595-1602.


• E. E. Barrera, S. Pantano, F. Zonta. A homogeneous dataset of polyglutamine and glutamine rich aggregating peptides simulations. Data in Brief 2021, 36, 107-109.


• R. Kist, L. F. S. M. Timmers, R. A. Caceres. Understanding the role of mTOR-mLst8 binding through coarse-grained simulation approaches. Molecular Simulations 2021, 47, 1198–1207.


• F. Klein, F. Sardi, M.R. Machado, C. Ortega, M.A. Comini, S. Pantano. CUTie2: The Attack of the Cyclic Nucleotide Sensor Clones. Froniers Molecular Biosciences 2021, 8, 629-773.

2020

• A. Marchetto, Z. S. Chaib, C. A. Rossi, R. Ribeiro, S. Pantano, G. Rossetti, A. Giorgetti. CGMD platform: integrated web servers for the preparation, running, and analysis of coarse-grained molecular dynamics simulations. Molecules 2020, 25, 24, 5934.


• F. Klein, D. Cáceres, M. A. Carrasco, J. C. Tapia, J. Caballero, J. Alzate-Morales, S. Pantano. Coarse-Grained parameters for divalent cations within the SIRAH force field. Journal of Chemical Information and Modeling 2020, 60, 8, 3935-3943.


• M. G. Herrera, M. F. G. Castro, E. Prieto, E. Barrera, V. I. Dodero, S. Pantano, F. Chirdo. Structural conformation and self-assembly process of p31-43 gliadin peptide in aqueous solution. Implications for celiac disease. The FEBS journal 2020, 287, 10, 2134-2149.

2019

• P. G. Garay, E. E. Barrera, S. Pantano. Post-translational modifications at the coarse-grained level with the SIRAH force field. Journal of Chemical Information and Modeling 2019, 60, 2, 964-973.


• E. E. Barrera, M. R. Machado, S. Pantano. Fat SIRAH: coarse-grained phospholipids to explore membrane–protein dynamics. Journal of Chemical Theory and Computation 2019, 15, 10, 5674-5688.


• M. R. Machado, A. Zeida, L. Darré, S. Pantano. From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field. Interface Focus 2019, 9, 3, 20180085.


• M. R. Machado, E. E. Barrera, F. Klein, M. Sóñora, S. Silva, S. Pantano. The SIRAH 2.0 force field: altius, fortius, citius. Journal of Chemical Theory and Computation 2019, 15, 4, 2719-2733.


• M. F. G. Castro, E. Miculán, M. G. Herrera, C. Ruera, F. Perez, E. D. Prieto, E. Barrera, S. Pantano, P. Carasi, F. G. Chirdo. p31-43 gliadin peptide forms oligomers and induces NLRP3 inflammasome/caspase 1-dependent mucosal damage in small intestine. Frontiers in immunology 2019, 10, 31.

2018

• A. Brandner, A. Schüller, F. Melo, S. Pantano. Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes. Biochemical and biophysical research communications 2018, 498, 2, 319-326.


• F. Zonta, D. Buratto, G. Crispino, A. Carrer, F. Bruno, G. Yang, F. Mammano, S. Pantano. Cues to Opening Mechanisms From in Silico Electric Field Excitation of Cx26 Hemichannel and in Vitro Mutagenesis Studies in HeLa Transfectans. Frontiers in molecular neuroscience 2018, 11, 170.

2017

• M. R. Machado, H. C. González, S. Pantano. MD simulations of viruslike particles with supra CG solvation affordable to desktop computers. Journal of Chemical Theory and Computation 2017, 13, 10, 5106-5116.


• E. E. Barrera, E. N. Frigini, R. D. Porasso, S. Pantano. Modeling DMPC lipid membranes with SIRAH force-field. Journal of Molecular Modeling 2017, 23, 259, 1-6.


• T. Calì, M. Frizzarin, L. Luoni, F. Zonta, S. Pantano, C. Cruz, M. C. Bonza, I. Bertipaglia, M. Ruzzene, M. I. De Michelis, N. Damiano, O. Marin, G. Zanni, G. Zanotti, M. Brini, R. Lopreiato, E. Carafoli. The ataxia related G1107D mutation of the plasma membrane Ca2+ ATPase isoform 3 affects its interplay with calmodulin and the autoinhibition process. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 2017, 1863, 1, 165-173.


• N. C. Surdo, M. Berrera, A. Koschinski, M. Brescia, M. R. Machado, C. Carr, P. Wright, J. Gorelik, S. Morotti, E. Grandi, D. M. Bers, S. Pantano, M. Zaccolo. FRET biosensor uncovers cAMP nano-domains at β-adrenergic targets that dictate precise tuning of cardiac contractility. Nature Communications 2017, 8, 15031.

2016

• M. R. Machado, S. Pantano. SIRAH tools: mapping, backmapping and visualization of coarse-grained models. Bioinformatics 2016, 32, 10, 1568-1570.

2015

• M. R. Machado, S. Pantano. Exploring LacI–DNA dynamics by multiscale simulations using the SIRAH force field. Journal of Chemical Theory and Computation 2015, 11, 10, 5012-5023.


• L. Darré, M. R. Machado, A. F. Brandner, H. C. González, S. Ferreira, S. Pantano. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. Journal of Chemical Theory and Computation 2015, 11, 2, 723-739.

2013

• H. C. Gonzalez, L. Darré, S. Pantano. Transferable mixing of atomistic and coarse-grained water models. The Journal of Physical Chemistry B 2013, 117, 46, 14438-14448.


• P. D. Dans, L. Darré, M. R. Machado, A. Zeida, A. F. Brandner, S. Pantano. Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level. Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics 2013, 71-81.

2012

• L. Darré, M. R. Machado, S. Pantano. Coarse-grained models of water. Wiley Interdisciplinary Reviews: Computational Molecular Science 2012, 2, 6, 921-930.


• L. Darré, A. Tek, M. Baaden, S. Pantano. Mixing atomistic and coarse grain solvation models for MD simulations: let WT4 handle the bulk. Journal of Chemical Theory and Computation 2012, 8, 10, 3880-3894.


• A. Zeida, M. Rodrigo Machado, P. D. Dans, S. Pantano. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations. Physical Review E 2012, 88, 2, 021903.

2011

• M. R. Machado, P. D. Dans, S. Pantano. A hybrid all-atom/coarse grain model for multiscale simulations of DNA. Physical Chemistry Chemical Physics 2011, 13, 40, 18134-18144.

2010

• L. Darré, M. R. Machado, P. D. Dans, F. E. Herrera, S. Pantano. Another coarse grain model for aqueous solvation: WAT FOUR? Journal of Chemical Theory and Computation 2010, 6, 12, 3793-3807.


• P. D. Dans, A. Zeida, M. R. Machado, S. Pantano. A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. Journal of Chemical Theory and Computation 2010, 6, 5, 1711-1725.