Citations

If SIRAH was beneficial to your work, please cite one or more of these SIRAH references:

  • 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

  • Darré, L.; Machado, M. R.; Brandner, A. F.; González, H. C.; Ferreira, S.; Pantano, S. 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, 723–739. Access the paper Citation

  • Machado, M. R.; Barrera, E. E.; Klein, F.; Soñora, M.; Silva, S.; Pantano, S. The SIRAH 2.0 Force Field: Altius, Fortius, Citius. Journal of Chemical Theory and Computation 2019, 15, 2719–2733. Access the paper Citation

In addition, please include the following citations if the following parameters were used:

  • Post-translational modifications:

    • Garay, P. G.; Barrera, E. E.; Pantano, S. Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field. Journal of Chemical Information and Modeling 2020, 60, 964–973. Access the paper Citation

  • Metal ions:

    • Klein, F.; Cáceres, D.; Carrasco, M. A.; Tapia, J. C.; Caballero, J.; Alzate-Morales, J.; Pantano, S. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. Journal of Chemical Information and Modeling 2020, 60, 3935–3943. Access the paper Citation

  • DNA:

    • Dans, P. D.; Zeida, A.; Machado, M. R.; Pantano, S. A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. Journal of Chemical Theory and Computation 2010, 6, 1711–1725. Access the paper Citation

  • Lipids:

    • Barrera, E. E.; Machado, M. R.; Pantano, S. Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane–Protein Dynamics. Journal of Chemical Theory and Computation 2019, 15, 5674–5688. Access the paper Citation

  • Solvent with simple electrolytes:

    • Darré, L.; Machado, M. R.; Dans, P. D.; Herrera, F. E.; Pantano, S. Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? Journal of Chemical Theory and Computation 2010, 6, 3793–3807. Access the paper Citation

  • Multiscale Simulations:

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

    • 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 Citation

If SIRAH Tools were used please cite:

  • Machado, M. R.; Pantano, S. SIRAH tools: mapping, backmapping and visualization of coarse-grained models. Bioinformatics 2016, 32, 1568–1570. Access the paper Citation

See also

If you wish to view some SIRAH applications, please visit the Further reading page.