Further Reading

SIRAH Applications

  • A current review of SIRAH:

    • Klein, F.; Soñora, M.; Santos, L. H.; Frigini, E. N.; Ballesteros-Casallas, A.; Machado, M. R.; Pantano, S. The SIRAH force field: a suite for simulations of complex biological systems at the coarse-grained and multiscale levels. Journal of Structural Biology 2023, 107985. Access the paper Citation

  • A current review of coarse-graining models and applications for proteins (including SIRAH):

    • Borges-Araújo, L.; Patmanidis, I.; Singh, A. P.; Santos, L. H. S.; Sieradzan, A. K.; Vanni, S.; Czaplewski, C.; Pantano, S.; Wataru Shinoda, W.; Monticelli, L.; Liwo, A.; Marrink, S. J.; Souza, P. C. T. Pragmatic Coarse-Graining of Proteins: Models and Applications. Journal of Chemical Theory and Computation. 2023. Access the paper Citation

  • Protein-DNA complexes and Membrane Proteins:

    • Calì, T.; Frizzarin, M.; Luoni, L.; Zonta, F.; Pantano, S.; Cruz, C.; Bonza, M. C.; Bertipaglia, I.; Ruzzene, M.; De Michelis, M. I.; Damiano, N.; Marin, O.; Zanni, G.; Zanotti, G.; Brini, M.; Lopreiato, R.; Carafoli, E. 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. Access the paper Citation

    • Brandner, A.; Schüller, A.; Melo, F.; Pantano, S. Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes. Biochemical and biophysical research communications 2018, 489, 319–326. Access the paper Citation

    • Zonta, F.; Buratto, D.; Crispino, G.; Carrer, A.; Bruno, F.; Yang, G.; Mammano, F.; Pantano, S. 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. Access the paper Citation

    • Barrera, E. E.; Pantano, S. Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBER. AIP Publishing, 2023. Access the paper Citation

  • DNA:

    • Zeida, A.; Machado, M. R.; Dans, P. D.; Pantano, S. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations. Physical Review E, 2012, 86. Access the paper Citation

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

  • Lipid Membranes:

    • Barrera, E.E.; Frigini, E.N.; Porasso, R.D.; Pantano, S. Modeling DMPC lipid membranes with SIRAH force-field. Journal of Molecular Modeling 2017, 259. Access the paper Citation

  • Intrinsically Disordered Proteins:

    • Klein, F.; Barrera, E. E.; Pantano, S. Assessing SIRAH’s Capability to Simulate Intrinsically Disordered Proteins and Peptides. Journal of Chemical Theory and Computation 2021, 17, 599–604. Access the paper Access the paper

  • Multiscale Simulations:

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

    • Darré, L.; Tek, A.; Baaden, M.; Pantano, S. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. Journal of Chemical Theory and Computation 2012, 8, 3880–3894. Access the paper Access the paper

    • Gonzalez, H. C.; Darré, L.; Pantano, S. Transferable Mixing of Atomistic and Coarse-Grained Water Models. The Journal of Physical Chemistry B 2013, 117, 14438–14448. Access the paper Access the paper

    • Machado, M. R.; Pantano, S. Exploring LacI–DNA Dynamics by Multiscale Simulations Using the SIRAH Force Field. Journal of Chemical Theory and Computation 2015, 11, 5012–5023. Access the paper Access the paper

  • Solvent:

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

  • Aggregating Peptides:

    • Barrera, E.; Chirdo, F.; Pantano, S. p31-43 Gliadin Peptide Forms Oligomers and Induces NLRP3 Inflammasome/Caspase 1- Dependent Mucosal Damage in Small Intestine. Frontiers in Immunology 2019, 10, 2792. Access the paper Access the paper

    • Barrera, E. E.; Pantano, S.; Zonta, F. A homogeneous dataset of polyglutamine and glutamine rich aggregating peptides simulations. Data in Brief 2021, 36, 107109. Access the paper Access the paper

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

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

  • Virus-Like Particles:

    • Machado, M. R.; González, H. C.; Pantano, S. MD Simulations of Virus like Particles with Supra CG Solvation Affordable to Desktop Computers. Journal of Chemical Theory and Computation 2017, 13, 5106–5116. Access the paper Access the paper

    • Soñora, M.; Martínez, L.; Pantano, S.; Machado, M. R. Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. Journal of Chemical Information and Modeling 2021, 61, 408–422. Access the paper Access the paper

    • Machado, M. R.; Pantano, S. Fighting viruses with computers, right now. Current Opinion in Virology 2021, 48, 91–99. Access the paper Access the paper

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

  • SARS-CoV-2 simulations:

    • Garay, P. G.; Barrera, E. E.; Klein, F.; Machado, M. R.; Soñora, M.; Pantano, S. The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations’ Dataset of the SARS-CoV-2 Proteome. Frontiers in Medical Technology 3 2021, 644039. Access the paper Access the paper

See also

SIRAH has a Google Scholar page, feel free to visit it and discover additional publications.